The Federal Government removed a respected veterinarian after she presented evidence of cruelty and appalling conditions on board Australian live export ships, according to documents obtained by the ABC.

Key points: Report by Dr Lynn Simpson revealed photographic evidence of animal cruelty

Report by Dr Lynn Simpson revealed photographic evidence of animal cruelty Dr Simpson was removed from her position weeks after the confidential report was inadvertently published

Dr Simpson was removed from her position weeks after the confidential report was inadvertently published Australian Livestock Exporters Council has denied industry bullies veterinarians, says report is outdated

Dr Lynn Simpson was one of the country's most experienced and respected live export veterinarians when she was hired by the Department of Agriculture in 2012 in response to the explosive Four Corners report on live export cruelty.

As a technical adviser to the Animal Welfare Branch, Dr Simpson was invited to submit a report to a government steering committee which was reviewing Australia's standards for live export.

WARNING: This story contains graphic images.

Dr Simpson's report, which she submitted in November 2012, was meant to be confidential.

It revealed photographic evidence of animal cruelty she had witnessed working onboard Australia's live export ships.

Cattle in overcrowded conditions on a live cattle export ship ( Supplied )

The report showed pictures of animals suffering and, in some cases, suffocating in overcrowded pens and drowning in faeces.

Dr Simpson detailed how cattle were forced to stand on hard floors for weeks on end, resulting in horrific leg injuries which often led to the animal being euthanased.

She also raised concerns that sick animals which would clearly be unable to survive the voyage were often loaded onto the ship because of poor inspection processes.

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Department published confidential report on its website

Dr Simpson told the ABC she was trying to be as honest as possible about the conditions she had witnessed during her 11 years on live export ships.

"The images that I showed were stuff that I would expect to see every voyage," she said.

A cow which died after getting its head stuck in a barrier on a live cattle export ship. ( Supplied )

"On these ships, I expect to see leg injuries, I expect to see pneumonia, I expect to see animals drenched in faecal matter."

The ABC has obtained documents that show Dr Simpson's report was meant to be an internal, confidential document not for public release.

But the department, not Dr Simpson, accidentally published the report on the department's website.

"That is when all hell broke loose and I went from being a valued employee to persona-non-grata," Dr Simpson said.

Dr Simpson found herself gradually isolated and her evidence sanitised.

"I was excluded from discussions, meetings and then they asked me to remove all photographic evidence from a report I had prepared for the Australian Maritime Safety Authority," she said.

The industry cannot work with you

Weeks after her report was published, she was removed from her position.

"I was gutted. It told me that the [live export] industry was controlling the regulator," Dr Simpson said.

"For the industry to be able to kick a government employee out of a government job, it speaks volumes, it is a form of corruption and that is all there is to it.

"I was a clean player in a dirty game, and I think it's disgusting they've shut me down."

The then first assistant secretary of the department's Animal Division, Karen Schneider, wrote a letter to Dr Simpson admitting that she was being sacked from her role in the Animal Welfare branch because of concerns from the live export industry.

"This is because the industry with which we engage has expressed the view that they cannot work with you," Ms Schneider wrote.

"I do not share the expressed views of industry … you have done [your job] competently and, as deputy secretary Philip Glyde and I have assured you … your technical expertise is valued by the department."

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RSPCA chief scientist Bidda Jones was also a member of the steering committee which received Dr Simpson's report.

"Lynn's treatment by the Government was appalling," she said.

"To me what has happened to her is indicative of the way the live export industry operates.

"They don't want the public to know what it is that this industry entails."

The Federal Government and the public servants who worked with Dr Simpson declined to comment.

Industry brands Dr Simpson's report 'ancient history'

Mr Crean has since apologised to Dr Simpson for the way she was treated. ( ABC News: James Thomas )

Former Labor leader Simon Crean, who has been the chairman of the Australian Livestock Exporters Council (ALEC) since 2014, denied the industry bullies veterinarians.

He has also said Dr Simpson's report was outdated, describing it as "ancient history".

"You have to acknowledge the investment that is being made, the improvement being made, and the preparedness by the industry to recognise the welfare of the animal has to be paramount," he told 7.30.

"I think there has been an important wake-up call to the industry and I don't think there has been evidence of these sorts of photos since.

"Anyone can trot out the old photo, talk about the past.

"We acknowledge that in the past mistakes were made. The issue is, are we prepared to learn from the mistakes and improve on them?"

In a subsequent interview, following 7.30's revelations of Australian cattle being sledgehammered in Vietnam, Mr Crean took a more conciliatory approach, offering Dr Simpson a qualified public apology.

"At no stage, did ALEC seek to pressure the department to have her dismissed," he said.

"Now that being said, I accept the fact that Dr Lynn Simpson has felt aggrieved by the treatment that she got.

"If that's the case then on behalf of ALEC, I apologise for it."

In a statement, ALEC CEO Alison Penfold said Dr Simpson "sought to provide constructive advice to exporters on improvements".

Ms Penfold referred to Mr Crean's comments, saying ALEC reiterated his apology and "that at no time did we seek Dr Simpson's dismissal".

"The Australian livestock export Industry is focused on utilising its levies on research, development and extension to address the key causes of morbidity and mortality towards our goal of zero harm, including those concerns raised by Dr Simpson," she said.

Dr Simpson is no longer working as a vet, however she says she has no doubts the live export industry is still plagued with animal welfare issues.

"This industry entails unnecessary pain and suffering for all the animals involved within it," Dr Simpson said.

"Anyone who tells you different is either ill-informed, they're a liar or they're staying silent for fear of losing their job."