The owner of Geronimo, an alpaca which was executed over Bovine TB fears, said government officials have refused to hand over the animal’s remains.
The eight-year-old alpaca was killed on 31 August by vets after being removed from a Gloucestershire farm by police.
The High Court ruled that Geronimo must be destroyed after twice testing positive for bovine TB.
Owner Helen Macdonald insisted the tests may have given false positives and launched a four year legal battle in an attempt to save her pet.
Macdonald wanted the Government to allow Geronimo to be tested for a third time or let him live to aid research into the disease.
Now, the farmer claims that she is unable to give the alpaca a funeral because the Department for Environment, Food and Rural Affairs (Defra) is holding onto his remains because of TB related reasons.
She said: “They will never give bodies back to owners or farmers where they suspect disease.
"It was never going to be an option for Geronimo to come home. They incinerated the ‘carcass’ as they referred to him.
Watch: Chief vet 'sympathises with Geronimo's owner
"They wanted me to arrange for him to be put to death so they could say I consented. They told me to tell them when he was dead so they could collect the ‘carcass’.”
MacDonald has now lodged a complaint with The British Alpaca Society after the alpaca was removed from her Gloucestershire farm using a rope around his neck instead of a head collar.
She believes that her beloved eight year old pet could have been accidentally throttled by Defra officials inside the van when he was removed from the farm.
She said: “I believe he was suffocated and strangled in the horse trailer and they have not provided video footage to the contrary.”
Defra says that experienced veterinary pathologists from the Government’s Animal and Plant Health Agency found a number of TB-like lesions during the initial post-mortem.
Chief veterinary officer Dr Christine Middlemiss said: “A number of TB-like lesions were found and in line with standard practice these are now undergoing further investigation.
“These tests include the developing of bacteriological cultures from tissue samples which usually takes several months - we would expect to complete the full post-mortem and culture process by the end of the year."
The department also said it is a legal requirement that the body of any animal suspected of TB infection must be disposed of properly and safely as part of disease control measures.
However, MacDonald has refuted these claims saying a post-mortem found no signs of TB.
Watch: War of words over Geronimo bovine TB post-mortem result