The official has also claimed that a number of investigations by Department inspectors were hampered by high-level political interference and vested interests.

In one case involving a Kilkenny-based company, Animal Farmacy, an investigation into what were described by an inspector as evidence of breaches of regulations was stopped in its early stages following representations to three senior politicians, including then taoiseach Enda Kenny.

There were also allegations against one of the investigators of corruption, assault and sexual harassment but two separate inquiries found they had no basis and no complaint was made to gardaí.

The Department's legal adviser had urged for the investigation into Animal Farmacy to proceed and be finalised because the case was "caught in a thick blanket of political fog".

In another case, it is alleged that a Department inspector was put under pressure from other senior officials not to give a statement to gardaí after a suspected fraud in An Bord Bia's quality assured scheme. The subsequent Garda investigation resulted in a conviction for a vet and two farmers being sent for trial.

The first disclosure was made to the then minister Michael Creed in August, 2017. It contained eight separate claims of wrongdoing and was investigated internally.

A report on the allegations was issued over three years later, last November, and found that the whistleblower had "not disclosed any evidence that a wrongdoing within the meaning of the Protected Disclosures Act 2014 had been committed by any of the individuals" named. The whistleblower was moved into a new role in the Department following the first disclosure.

A second disclosure to the TD Catherine Murphy, containing further allegations, was made in July 2020. No findings have yet been made.

The most recent disclosure by the official was made three weeks ago, again to Ms Murphy. It deals with charges of animal cruelty against a Monaghan farmer which were dropped just days before the case was to be heard in the District Court last month.

Among the allegations, it is claimed that local TD Heather Humphreys passed on a letter to the Department about the case. Humphreys subsequently confirmed this, but said she had not interfered in the case.

Other cases in the last four years detailed in the protected disclosures concerned a major fraud in the milk quota scheme and a prescription fraud to the tune of €70,000 plus VAT.

The full texts reveal a litany of abuses of regulations and law by vets, farmers and others - as well as allegations that investigations were not properly pursued. They paint a picture of favourable treatment to some over others, political interference in serious matters and of a Department which has been scaling back the number of investigations it is carrying out into fraud and corruption in the Irish food and agriculture industry.

A spokesperson for the Department of Agriculture, Food and the Marine said last Friday that it "takes its regulatory and prosecutorial function very seriously and for this reason is anxious to ensure that objectivity is always at the core of its decision-making in this area".

The spokesperson added: "Objectivity is absolutely necessary for the responsible exercise of this important aspect of the Department's work and all decisions based on Department investigations are fair and based on the public interest whether concluded by way of a criminal prosecution or otherwise."

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'John Doe' took a last drag from his cigarette, stubbed the butt into a tray and stepped from the terrace to the laptop on his desk. It was a balmy summer's evening in August 2017 and he had spent months thinking about his job at the Department of Agriculture and the right thing to do about some very inconvenient truths.

Now he was doing it: "Dear Minister, pursuant to the Protected Disclosures Act 2014, I wish to make the following Protected Disclosures..."

For four months he heard nothing, then he got a call from a Department official who had been assigned to investigate.

A month later they met for the first time. Two years after that - a Friday afternoon in February 2020 - they met again.

How are you, he said.

Good to see you, she said.

How's it going, he said.

Not too bad, she said.

And for five minutes they continued to exchange pleasantries until the humming and hawing started.

That's when he knew.

"So look," she said.

"So look'" is never good.

"I just wanted an opportunity to have a chat with you again, to let you know what I've been looking at, and where I would think, hopefully we can progress."

"Hopefully" wasn't promising.

"So, I have reviewed a substantial amount of material related to the things that you have brought to my attention."

She was dragging it out.

"I know that you probably would have seen a good bit of that material as well. Umm, I've had the benefit, I suppose, of having seen the material unredacted."

What had she seen?

"Umm… Now, from what I have looked at so far, I haven't been… I haven't seen any evidence of wrongdoing."

How hard had she looked?

"Umm, but the question is," she said, "where do we go from here?"

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The Department of Agriculture and Food said it expected to close its files on the €165,000 Cooley peninsula ewe premium fraud uncovered during the foot-and-mouth crisis by the end of the month. However, no prosecutions have been taken yet against about 20 farmers who had submitted false claims for 2,000 ewes which were found to be bogus when the peninsula's flocks had to be slaughtered in late March last year.

The fraud came to light when a movement ban was imposed on the area to prevent the spread of the disease following the outbreak in Proleek on the Louth-Armagh border and all the animals on the 275 farms in the area were slaughtered. The sheep farmers in the Cooley area had submitted claims for 37,165 ewes that year but when the slaughter took place, only 30,540 ewes could be located.

Sean MacConnell,

The Irish Times,

August 17, 2002

Whistleblower legislation, introduced in 2014, protects people who raise concerns about wrongdoing in their workplace. Because he does not want his identity known to the wider public, he is 'John Doe', or JD, in this article.

He was born and raised on a farm, spent four years in Dublin completing a degree in veterinary medicine and began his career at the Department of Agriculture in 1999 as a veterinary inspector (VI) in Louth. That's where he learned to swear.

In the Wee County there were big problems: sheep and cattle being shuffled across the Border from North to south and south to North; farmers scamming payments for herds that didn't exist; vets doctoring paperwork and inventing prescriptions; pharmacists dealing in antibiotics and angel dust.

He remembers an early case - a compensation claim for a herd of cattle infected with brucellosis on a farm outside Dundalk.

He escorted the herd to an abattoir, supervised the slaughter, and returned to his office in Drogheda to examine the ID tags. The case stank. There had been no brucellosis in the county for years. Why now?

He sent the tags to the Garda forensic laboratory and when the results came back his suspicions were confirmed - the farmer had cattle on both sides of the Border and had shuffled the herd from the North and switched the tags.

Catching the cowboys was one thing, bringing them to justice was another. First you put a file together, collecting statements and maintaining a chain of evidence; then you identified the appropriate charges.

The file was sent to the Chief State Solicitor and passed to the local State Solicitor, who engaged a barrister.

If the barrister was happy, he'd draft the summonses and send them back for checking. Then they'd go back to the State Solicitor to be issued by the local court before being sent to the gardaí for serving. But even that was rarely simple.

The brucellosis scammer, for example, was resident in the North and a clause in the Good Friday Agreement was invoked so the summons could be served by the RUC. But these people rarely came quietly. "Get the f**k out of my yard!" was a standard greeting. He was thumped, spat at, rammed, and had a gun pointed at him.

It took courage to take them on, and a firmness often misinterpreted as rudeness or abrasiveness when he sought information. As an authorised officer he was entitled to information. His job was the law. The law was black and white. But people didn't always appreciate that.

It's not a job for everyone but it got him the attention of the Special Investigations Unit (SIU) where his new boss was a kindred spirit called Pat Brangan. He spent his first months with the unit in Naas, was redeployed to Dundalk for the foot-and-mouth crisis and spent two years in Mullingar on a joint operation with the gardaí.

A farmer in Mayo was defrauding the State of thousands in beef premia; a dealer from Louth was smuggling cattle and pumping them with hormones and steroids; a farmer in Meath was scamming tags and had a hundred cattle on his land with incorrect identities. All were successfully prosecuted. And it was this that set him apart.

It was a running joke at the unit that 'John Doe' should have been a barrister. He had an encyclopaedic knowledge of the systems and the legislation and would spend hours sometimes with a file on his lap and his feet on his desk, running the angles through his forensic brain: 'What's missing here?' 'Why is it missing?'

And for those first 12 years he loved it. Because it mattered. The medications stocked by the pharmacies mattered. The signatures on the prescriptions mattered. The raids on the farmers and the dealers mattered. The SIU mattered. What they uncovered mattered.

He recalls a judge's summation once before jailing a farmer for tampering with tags. "This type of offence is terribly serious," he said, "endangering the health of the nation, the confidence of the consumer, the integrity of the export system and the capacity to deal with outbreaks of disease."

This was the truth of it. To change the identity of an animal was to change everything about it - disease history, movement history, medications history. And it was a truth heavily endorsed by the suits in Leinster House and the marketing men at Bord Bia and the Irish Farmers Association.

Farm to fork, they said. Taste the island, they said. Not all food is the same, they said. The Quality mark ensures your food has been verified at every stage, they said. Your food is our passion, they said. Buy Irish, they said. It means you can enjoy it even more because you can trust it, they said. It makes him laugh.

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If you're tired of driving to multiple outlets for food, toys, supplements and veterinary services with an eager dog or wary cat in the back of your car then look no further because here at Animal Farmacy we offer a unique service provided by the combined passion, experience, knowledge and expertise of pharmacists Joseph Haire and Clare Hughes along with head of operations, Trish McOwan, and veterinary technical adviser Rachael Hampton.

Based in The Hub, Cillin Hill, on the outskirts of Kilkenny City, we act as a one-stop-shop that caters for your animal needs including livestock, equestrian and pets. Through the Kissane Pharmacy chain we sell animal health products and we are fully regulated and compliant with an in-store vet who is available, on call, 24 hours a day. As well as providing animal care products at exceptionally competitive prices, we also offer expertise in herd health management.

Ad for Animal Farmacy in 2012

[Note: this company has no connection to Animalfarmacy.ie, an online retail business based in Co Meath.]

Animal Farmacy Ltd was a licensed merchant and veterinary practice. It was not a licensed pharmacy but two of the owners were pharmacists, and it was connected to a pharmacy in Thomastown. That wasn't unlawful but it wasn't conventional and raised some potentially messy issues.

The issues were first highlighted in a letter from the Department of Agriculture following a routine inspection in April 2011.

The company was reminded that while it was fine for the retail store and veterinary practice to share the same premises, the businesses had to be separate entities, with separate stock and separate records and a separate door.

Injectable antibiotics, for example, destined for use in the veterinary practice, had to be ordered by the vet working there; the retail store could not order any product on behalf of the veterinary practice and all animal remedies supplied to the veterinary practice from wholesalers had to be addressed on the invoice to the veterinary practice.

Eight months later, when the Department visited again, there were further discrepancies: two prescription-only medicines (POMs) were found in the store; the door between the store and the practice was closed but not locked and there were concerns about the transfer of POMs between the practice and the pharmacy in Thomastown.

Then it did get messy.

It started when Rachael Hampton, the vet employed by Animal Farmacy, was invited to meet with Department officials at their regional office in Waterford. She was heavily pregnant at the time but happy to attend, until her employers insisted she couldn't go alone and would have to be accompanied by one of the partners. Then Animal Farmacy sent a letter to the Department from their solicitors. That's when JD got the call. "Go and take a look," Brangan said.

Department inspections are always double-handed and his assistant on the morning of February 22, 2012, was a bright veterinary inspector from the regional office who had visited the premises before. They liaised with Trish McOwan and began with a brief tour, checking the product on the shelves.

There was a fridge in a storage area at the back with a container of Bovidec, a vaccine used on cattle for Bovine Viral Diarrhoea (BVD). It's a classified drug - 'prescription-only medicine exempt' - and its sale or supply is restricted to veterinary practitioners or pharmacies. But that's not where they found it. "This shouldn't be here," JD said.

McOwan tried to explain that customers didn't have access to that part of the store and that the container was clearly marked 'overflow from vet fridge'. JD removed the container from the fridge and suggested they go next door and ask the vet.

Hampton was on maternity leave and had been replaced by a locum, Anja Norman. The locum said she knew nothing about the Bovidec and started shaking her head when McOwan tried to explain it. JD ordered the manager to leave, then took a statement from Norman.

"I am a registered veterinary surgeon… [JD] has shown me nine boxes of Bovidec ARA 383482 to ARA 383490 inclusive. These do not belong to the veterinary practice. I accept that [JD] found the above Bovidec in the fridge in the Licensed Merchant part of Animal Farmacy Ltd. I did not know it was there. I did not write 'Overflow from Vet Fridge' or 'Overflow from Vet' on the box. If I had put it there, I would have been aware of it and there would have been a reason."

Rachael Hampton wasn't aware of it either. She took a call from Norman, drove to the store with her husband in the afternoon, and told JD she was unhappy with some of the practices there, had felt pressured at times to sign prescriptions, and intended to resign after her maternity leave.

That the locum had already quit (after giving her statement) created a problem for Animal Farmacy: with no vet present to accept responsibility for the restricted medicines, they would have to be seized.

The inspectors began an inventory and started packing and an arrangement was made to return the drugs to a supplier. They had uncovered evidence of other possible breaches: the supply of a prescription-only medicine in the absence of a valid veterinary prescription; the mail order of a prescription-only medicine without a licence; and evidence of wholesaling between the retail store and the veterinary practice, and between the veterinary practice and an associated pharmacy.

It was late when Animal Farmacy's director and shareholder arrived. JD doesn't recall Joe Haire saying much, but Clare Hughes was confrontational: What was going on? Why weren't they given time to recruit another vet? Where was the Bovidec? Were they aware she was a QP (qualified person)? Did they know what that was?

He found out later she was recording them.

It was after 7pm when JD eventually clocked out. Cillin Hill was dark and deserted. He was sure he had parked behind a footpath and didn't notice the SUV in his wing mirror as he reversed.

It was nothing much. A minor tip. He examined both cars but couldn't see any damage - a small crack in the bumper was later revealed - then went back into the store to ascertain and alert the owner of the car.

It was Clare Hughes.

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It was good speaking to you yesterday Mr Reddy and apologies for missing your call An Taoiseach. However I would like to thank you for returning my call; to be honest it gives us great faith in the system to get political support and feedback following the events of the last few weeks and the highly questionable behaviour of the Department of Agriculture.

The shareholders of Animal Farmacy are very aggrieved by the Department of Agriculture and particularly the Special Investigations Unit's (SIU) inappropriate response and actions to what appears to be concerns of the company structure rather than compliance, that could and should have been handled via arbitration and mediation rather than harassment, false accusation and intimidation of us and our customer base the farmer.

Email from Clare Hughes to Nick Reddy (private secretary to Enda Kenny) sent on March 16, 2012

If 20 years in the SIU teaches you anything, it's that there's one thing to be said for people who come running at you with a pitchfork screaming, "I'll burst your f***ing face" - you know exactly where you stand. That was the thing about the weeks and months that followed - he had no idea what was coming at him.

It started a week after the inspection when solicitors acting for Animal Farmacy lodged a plenary summons with the High Court seeking, among other things, the return of all goods and medicines seized, as well as aggravated and exemplary damages. He took a call from 'Ag House', sent a report and thought no more of it - they'd dealt with plenty over the years from disgruntled traders and farmers.

So it was business as usual - well, almost. Pat Brangan had retired after a long and distinguished career and been replaced by Brian Flaherty. The investigation continued. He collated a mountain of paperwork from Animal Farmacy and spent weeks cross-checking invoices and taking statements from clients.

Then he was told to stop. He remembers the moment vividly - a call from Flaherty as he was driving towards Gowran on a Friday afternoon. A complaint had been made. Flaherty had never seen the like of it. Seven or eight pages, he said. A meeting had taken place at a very senior level, he said. Don't do anything further with regard to the investigation, he said.

The sweating started a week earlier (March 16), with a letter from David King (Assistant Private Secretary to the Taoiseach) to Tom Moran (Secretary General at the Department of Agriculture): "I refer to Nick Reddy's telephone call to you on 15th March, 2012 regarding Animal Farmacy Ltd. I have attached the correspondence that was given to the Taoiseach. The Taoiseach has asked if you could look into this matter and revert to him."

Then Joe Haire raised the temperature with a letter to Richard Bruton (Minister for Jobs, Enterprise and Innovation): "I have no doubt that these inspections are motivated by market interference rather than any real concerns with regulatory compliance. You would have to wonder at the behaviour of these government officials, the harassment and bullying of the staff and customers of a legitimate business.

"It certainly has little to do with the pursuit of excellence in public office."

Then Clare Hughes followed up with an email to the Taoiseach: "I hope you returned safe and sound from your trip to the US, congratulations, all reports seemed to indicate a very successful mission. Please see a copy of a letter sent to Minister Bruton this morning (cc Minister Coveney) which details our concerns, grievances and our belief to be the true remit of the SIU."

Then Moran sent a memo to his deputy, Philip Carroll: "I sent you papers in relation to the above sent to me by the Taoiseach's office. Before any examination of the methodology and the issues raised in relation to the investigation of this company as described by the company, could you please find out from Martin Blake (Chief Veterinary Officer) and from the Division the basis for the investigations in the first place. When this has been established, I would like to discuss the steps we should take."

Then JD got the order to stop.

Three days later (March 26) solicitors acting for Hughes sent a letter to Agriculture House: "Please find enclosed a copy of a letter which we have sent to [JD] arising from a traumatic incident which occurred on 22nd February 2012 at Cillin Hill. In the course of an investigation our client's car was damaged by [JD]. He denied damage at the time and was abusive and intimidating towards our client.

"Arising from the incident, our client suffered great stress and trauma and is still upset from it. Whilst our client has no difficulty with any reasonable investigation into her business and affairs, she takes grave exception to the bullying, harassment and intimidation which she suffered from [JD] on that occasion and we have no doubt but that the conduct of [JD] was excessive and traumatic for Ms Hughes.

"You might note that it is our client's intention to pursue [JD] and the Department of Agriculture for personal injury, loss and damage which she sustained and we invite you to admit responsibility and agree to compensate our client, in default of which, an application will be made to the Injuries Board on behalf of our client."

Then things started to boil.

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Deputy John McGuinness asked the Minister for Agriculture, Food and the Marine if he has confirmed in writing to a company (details supplied) in County Kilkenny the reasons the special investigation unit is carrying out an investigation into the company; if the company has been informed as to the reason the customers of this business have been contacted directly by the SIU; if he will confirm if any breach of regulation or law was notified to the company prior to inspection; if he will accept responsibility for the damage caused to a vehicle owned by the company; if every effort will be made by him to complete the investigation efficiently and in co-operation with the company in order to protect the five jobs involved; and if he will make a statement on the matter.

Parliamentary Question 495, March 27, 2012

A day after McGuinness posted PQ495, JD was sent a copy of the complaint. Or at least part of it. It comprised a cover letter from Trish McOwan; a two-page 'overview'; a page with details and dates; and three pages on the inspection from the SIU that ended mid-sentence.

He took a green pen from his desk and went through it line-by-line making notes in the margins… 'not true'... 'not correct'... 'absolutely wrong'...

Then he sent a 10-page report to Ag House: "The complaints represent a significant misrepresentation of facts and events," he wrote. "These complaints coincide with a Plenary Summons and threats of legal actions for damages/personal injuries etc as well as a Parliamentary Question. There is compelling evidence that this company has breached the Regulations…

"It is to be noted that, despite all the allegations of threatening behaviour… by Clare Hughes and Trish McOwan that they did not call the gardaí. It is also to be noted that Clare Hughes is threatening to claim damages including for 'Personal Injury' despite not being in the vehicle. The company has confirmed that it has surreptitiously recorded the inspectors; if such a recording exists they should be asked to produce it."

Animal Farmacy wasn't backing down. A week after Simon Coveney's response to McGuinness ("I am constrained from commenting in any detail about this matter because an investigation by my Department is ongoing') Joe Haire, sent an email to Leinster House: "Dear Minister Coveney, I must take issue with your answer to PQ495 last week… To my knowledge at least some of the elements of this so-called investigation has been brought to your attention so I am shocked to read 'that any investigations carried out by my Department are subject to the investigating powers set out in the relevant legislation'.

"There is no possible way that the nature and ferocity of this 'investigation' is provided for in the relevant legislation. The legislation does not permit officials to presume guilt, to defame, to intimidate, to harass and to bully in particular our thoroughly professional female veterinary surgeon (in late pregnancy), our female practice manager and female customers.

"Equally as important (bold) the legislation does not provide for price regulation or price protection by veterinary officials of your Department.

"We know, our suppliers know, the IFA know, our customers know, our elected representatives know and the dogs in the street know that these (bold) local veterinary officials of your Department are attempting to shut down our business to offer favour to friends and professional colleagues who are in direct competition with our business."

JD's rebuttal was also being assessed and part of a file sent up the line to Randall Plunkett, head of legal services at Agriculture House. The lawyer opined that Animal Farmacy and its directors "may have serious questions to answer" and advised that the investigation proceed and be finalised as soon as possible.

"The issues here are currently caught in a thick blanket of political fog," he wrote. "By getting the case into court we will quickly move to a more rational consideration of the issues, where the law will be considered and applied without political pressure."

But the law was not considered. The investigation remained on hold as the Department awaited the delivery of another report, which JD was told was in line with best practice. Pat Meskell, a senior superintendent veterinary inspector, began his appraisal with a trip to Animal Farmacy.

There was a favourable response to this visit. An email to Simon Coveney on April 11, 2012 co-signed by Joe Haire, Clare Hughes and Trish McOwan, read: "We acknowledge the appointment of Pat Meskell to review the behaviour of his Department colleagues in their many contacts with our business. We have found him to be fair and impartial to date."

But when the report was delivered, these were the key findings:

"Animal Farmacy was not targeted for inspection because of pressure from competitors. The investigating officers had obtained evidence that indicated that animal remedies regulations were not being observed."

"Signed statements from both veterinary employees confirm that there was interference by Animal Farmacy management in their role as veterinary surgeons, that they had been pressured to act unethically and, in at least two instances, illegally (this refers to a VS being asked to sign a script for an animal remedy that had been dispensed up to two days previously). One VS complained that she had been pressurised to make a diagnosis and to prescribe remedies over the telephone for animals that she had not seen."

"There have been in total four audits/inspections/investigations of AF not 13 as claimed by Animal Farmacy during my meeting with them."

"Both VS stated that they were unhappy with their roles in Animal Farmacy. This was mainly because of requests and demands being made of them that they considered unethical."

"There is some evidence that Animal Farmacy employees may have felt aggrieved as a result of being questioned by the (Department) officers. One VS did say that [JD's] initial approach was intimidating but went on to say that her subsequent dealings with him were satisfactory and proper, and that her signed and witness statement still stands."

"The visits to clients were all related to findings at the previous inspections of Animal Farmacy. These were standard follow-up visits and cannot be considered to be targeted harassment."

"There is no evidence that any of the (Department) staff were acting on behalf of any competitors of Animal Farmacy."

It was a vindication for the investigators, a validation for the Department, and should have been a green light for the investigation to resume.

But the report did not recommend the legal route as the only way forward. There was another option. The Department could suspend proceedings with regard to prosecution provided Animal Farmacy "gave a commitment to comply with the regulations, and to co-operate fully with all audits and inspections". It was also proposed - "in order to allow a new relationship to develop" -that these future inspections could be conducted by officers other than those previously involved. But what message would that send to the officers who had been involved?

Having had an opportunity to read Meskell's report, JD sent an email to his boss: "I await your direction as to whether or not I am to resume the investigation with a view to submitting a file to the State Solicitor. In relation to this company's apparent threat to litigate, I am satisfied that they have no basis. It is simple scaremongering. Had they a legal basis, they would have followed through on their plenary summons."

But the "thick blanket of political fog" wasn't lifting any time soon. An email from the Office of the Taoiseach to Tom Moran (Secretary General Dept of Agriculture) on August 5, 2012: "The Taoiseach, Mr Enda Kenny TD, has asked me to refer to a representation that he received on behalf of (Animal Farmacy Ltd). The correspondence was sent to your Department on March 16, 2012. I would be grateful for your advice as a matter of urgency as to the current position in this regard."

A month after that…

An email from the Secretary General's office to the Chief Veterinary Officer, Martin Blake: "The Secretary is anxious to bring the (Animal Farmacy) case to conclusion. He has asked if you would update him on the current position on your return. We will need a draft letter from the SG to the Taoiseach with a draft reply from the Taoiseach to (Animal Farmacy). We had another reminder from [the] Taoiseach's office this week. Also replies to representations to the Minister will have to be prepared."

A week later…

An email from the Office of the Taoiseach to the Secretary General: "I refer to previous correspondence on behalf of (Animal Farmacy Ltd - copy attached) and would appreciate if you could provide a draft reply for the Taoiseach's signature as soon as possible."

A month after that, on October 22, 2012 … An email from the Office of the Taoiseach to the Secretary General: "I refer to previous correspondence on behalf of (Animal Farmacy Ltd - copy attached). The Taoiseach wishes to reply in this matter immediately. Perhaps, therefore, you would provide a draft reply for the Taoiseach's signature as a matter of urgency." The investigation remained on hold. The frustration of the investigators grew.

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"Does [JD] not realise that all powers that he has should be used for criminal issues and not for minor offences?"

Statement attributed to John Bryan, president of the IFA, in the Meskell report. It also quotes him as saying that the Animal Farmacy practice was "fully compliant" and that the investigation was "over the top".

Minor offences can have major consequences when it comes to the business of food. In November, as the correspondence continued between the Office of the Taoiseach and the Department on Animal Farmacy, a series of tests were being conducted on beefburgers and ready meats in supermarkets by the Food Safety Authority of Ireland (FSAI).

What they found was astounding. One beefburger sample from Tesco turned out to be 29pc horse.

"I couldn't believe it," Alan Reilly, the CEO, told the London Independent.

"I thought, 'You can't have horse meat in beefburgers.' We were aware of the consequences for Ireland as a producer of safe and wholesome food; we were aware of the potential damage here."

Horses are routinely treated with an anti-inflammatory drug called phenylbutazone. The regulations require that all horses prescribed the drug are excluded from the food chain. This arises from fears regarding the possible carcinogenicity of phenylbutazone and it's a responsibility of vets prescribing the drug to record it on the horse passport.

In her second email to Enda Kenny - the one congratulating him on his successful mission to the US - Clare Hughes wrote about the harassment of a client at Animal Farmacy. The client was a woman. The woman had a horse. The horse required medication. The medication required a prescription. The prescription required a vet. The vet signed the prescription.

Why had this woman been subjected to four inspections from the SIU?

There is a story about the prescription, the vet and the client in the Meskell report. The prescription was for 30 sachets of phenylbutazone. The vet, Anja Norman, worked for Animal Farmacy. The client had horses. The vet did not attend these horses. The client did not have a prescription when the phenylbutazone was dispensed at Animal Farmacy. The horses' passports were not stamped.

Anja Norman wasn't happy. She didn't work that Saturday and told JD she had been pressured into signing the script retrospectively. She had also, she said, written to the client about the requirements for the passports but hadn't seen any yet.

So the inspectors went to see the client. If the client had co-operated and simply answered their questions there would not have been a second visit, but almost everything was a problem: she said the inspectors had no right coming into her yard; she claimed she had done nothing illegal; she was not in Kilkenny on the Saturday the phenylbutazone was obtained; she would not be making a statement and was taking legal advice.

So they went to see her again.

By the fourth visit, JD had established that three of the horses given phenylbutazone had been sold to the US. On March 21 he sent an email to his boss: "The passports are not now available. The vet in Animal Farmacy retrospectively signed the prescription but never received the passports to ensure they were marked not for human consumption. Should we notify the US authorities or do we need further information?"

Two days later, as he was driving towards Gowran on a Friday afternoon, he was ordered to stop the investigation. He didn't know then that it would never resume.

On May 22, 2013 - four months after the horsemeat scandal made headlines - the Department sent an email to staff advising that "following prolonged discussions involving the office of the (State Solicitor) and solicitors acting on behalf of Animal Farmacy Ltd, [the Department] and AFL have come to an agreed position in respect of matters arising from the inspections and investigation that took place in late 2011 and early 2012".

There was also an outline of the terms. Animal Farmacy had:

• Issued a Notice of Discontinuance in respect of proceedings it lodged against the Minister and the Attorney General.
• Confirmed that the proceedings were concluded.
• Agreed not to serve or issue any further civil proceedings against the Minister or any of his officials in respect to the investigation carried out.
• Withdrawn all allegations made regarding officials of the Minister in relation to the conduct of their investigation.

The Department had:

• Confirmed that the investigation was concluded and that the Department had no outstanding issues with Animal Farmacy Limited.
• Confirmed that the officers involved in the investigation that led to AFL issuing proceedings would not be deployed in future to engage with AFL or its directors.

On Friday, a spokesperson for the Department of Agriculture, Food and the Marine said that "the circumstances of every investigation undertaken by the Department are carefully and objectively considered with a view to arriving at a rational determination as to how the investigation can most effectively be resolved from a regulatory perspective".

The spokesperson added: "Objectivity is absolutely necessary for the responsible exercise of this important aspect of the Department's work and all decisions based on Department investigations are fair and based on the public interest whether concluded by way of a criminal prosecution or otherwise."

Clare Hughes, Joe Haire and Trish McOwan did not respond to queries sent to them by the Sunday Independent last week. The Department of the Taoiseach and Enda Kenny also did not respond.

When informed of the outcome, the two officers involved felt betrayed. JD responded with an angry note to his bosses: "The deal as described leaves it open for Animal Farmacy to accuse [the other officer] and myself of behaviour necessitating our removal from any future investigation into them or their directors. It is a bizarre precedent to set… Again, this demonstrates to me the political imperative of appeasing Animal Farmacy at all costs and ignoring any duty of care towards [the other officer] and myself."

His colleague concurred. "I must admit to being extremely disappointed and completely demoralised by the conclusion/outcome of this whole sorry saga," he wrote. "Implicit on my being 'stood down' is that someone somewhere does believe that I and my colleagues are guilty of some sort of misconduct.

"What allegations were made against me and what evidence was submitted to substantiate these allegations? I have not been afforded the opportunity to defend my good name and reputation…

"Kilkenny and its environs is a small place. I have no doubt that word of the collapse of the (Department) investigation into Animal Farmacy and the successful tactics employed by them to bring about that collapse will soon be common knowledge among those engaged in the Animal Remedies retail sector in the locality and beyond…

"The inspected can now effectively nominate the inspectors! If they don't like the outcome they can embark on this strategy of aggressive engagement with (the Department). I fear the consequences for our 'Food Island' reputation and for our general economy will be catastrophic."

For the Special Investigations Unit, it was the beginning of the end.

Next week - Part two of Paul Kimmage's report