Geronimo the alpaca has been culled by Government vets carrying out a court-ordered destruction warrant.
The animal was rounded up on Tuesday morning as other alpacas watched on from a nearby field, before being loaded into a trailer, which then left the farm near Wickwar, South Gloucestershire.
Defra said Geronimo was euthanised by staff from the Animal and Plant Health Agency (APHA) in order to control the spread of bovine tuberculosis.
Geronimo had twice tested positive for bovine tuberculosis and a destruction warrant had been ordered for the animal, although owner Helen Macdonald believed the tests had returned false positives and thousands of members of the public backed her plea to halt his culling.
Downing Street has expressed sympathy for Ms Macdonald, with the Prime Minister’s official spokesman saying: “It’s obviously highly distressing for someone to lose animals to TB and that’s a situation that farmers sadly have to face.
“Our sympathies are with Ms Macdonald and any others that are affected by this terrible disease.”
Avon and Somerset Police officers attended the site shortly before 11am on Tuesday alongside a number of people dressed in blue overalls, masks and goggles.
After around 20 minutes the black alpaca was led away by the officials from the APHA, flanked by police officers as press photographers captured the moment.
Chief veterinary officer Christine Middlemiss said: “This is a terribly sad situation and our sympathies remain with all those affected by this devastating disease.
“No one wants to have to cull infected animals if it can be avoided, but we need to follow the scientific evidence and cull animals that have tested positive for bTB to minimise spread of this insidious disease and ultimately eradicate the biggest threat to animal health in this country.
“Not only is this essential to protect the livelihoods of our farming industry and rural communities, but it is also necessary avoid more TB cases in humans.”
Defra said a post-mortem examination will be carried out by veterinary pathologists from the APHA.
Supporters had been camping out at Ms Macdonald’s farm to try to prevent officials arriving to destroy Geronimo and some were seen talking to police as the animal was removed.
One woman was briefly arrested after spraying officers with a water pistol, but was quickly de-arrested.
A spokesperson for Avon and Somerset Police said: “We can confirm officers are in attendance at a farm in the Wickwar area of South Gloucestershire this morning to support the Animal and Plant Health Agency (APHA), who are executing a court warrant.
“We’ll always support our partner agencies to carry out their lawful duties and our role is to prevent a breach of the peace and to ensure public safety is protected.”
Ms Macdonald had called on the Department for Environment, Food and Rural Affairs (Defra) to allow Geronimo to be tested for a third time or let him live to aid research into the disease.
Geronimo’s owner had argued that the Enferplex test is fundamentally flawed and said Geronimo tested positive because he had repeatedly been primed with tuberculin – a purified protein derivative of bovine TB bacteria.
The veterinary nurse received support from around the world – with more than 140,000 people signing a petition against Geronimo’s destruction.
Earlier this month, a High Court judge refused her lawyer’s application for a temporary injunction to stop the destruction order and reopen the case.
As well as alpacas, badgers have been a victim of the fight against bovine TB, with mass culling employed to stop the spread since 2013, sparking a huge public backlash.