The alpaca who tested positive for bovine tuberculosis twice, and was on a death row in the UK was killed.
The Department of Food, Environment and Rural Affairs (Defra) ordered Geronimo to be euthanized.
Owner Helen Macdonald disputed the results and mounted several High Court challenges to save him.
“I am absolutely disgusted by this government. These are barbaric actions. It’s a disgrace,” said Ms Macdonald, who added she had received no warning.
Defra staff dressed in blue overalls, goggles and masks, accompanied by police, arrived at her farm in Wickwar, near Bristol, at about 11:00 am and led Geronimo away to be destroyed, with the scene broadcast on an online live feed of the enclosure.
A spokesman confirmed the destruction warrant had been carried out after Geronimo was taken away from his pen and loaded into a trailer. The vehicle then left the scene under a police escort, with a number of protesters watching on.
Ms Macdonald said the government had refused to act in good faith and had ignored her consistent pleas for constructive dialogue.
“We know now they have been stringing us along for the last week, fobbing us off by saying people are on holiday and would get back to us this week.
“In fact, all the time they were simply planning to murder Geronimo. This is yet another appalling demonstration of bad faith and duplicity by the secretary of state and everyone at Defra,” she said.
“Geronimo has been manhandled out of my farm. He was rounded-up and dragged into a horsebox,” added Ms Macdonald.
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.
Once Defra staff had entered her farm earlier, Ms Macdonald tweeted to ask for an “urgent meeting” with Environment Secretary George Eustice before adding: “Please don’t execute Geronimo.”
Ms Macdonald, a veterinary nurse, had called on Defra to allow Geronimo to be tested for a third time or let him live to aid research into the disease.
She argued the test used to test Geronimo was flawed and said he had tested positive previously because he had repeatedly been primed with tuberculin – a purified protein derivative of bovine TB bacteria.
She lost a last-ditch High Court appeal to save Geronimo on 18 August, and the destruction warrant gave Defra until 4 September to put down the alpaca.
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.”
Defra said 28,356 cattle were compulsorily slaughtered in England in the 12 months to March 2021, after testing positive for bovine tuberculosis.
During 2020, a total of 205 camelids – animals such as camels, llamas and alpacas — were culled.