The first year of two pilot badger culls cost £3,350 for every badger killed, official figures show - but campaigners have claimed the true cost was more than £5,000 for each animal.
The pilots, in which 1,879 badgers were killed in Gloucestershire and Somerset, cost the taxpayer £6.3 million in their first year, the figures reveal.
The Government said the costs were largely due to rigorous monitoring of the humaneness and efficacy of the culls, with £2.6 million spent on humaneness monitoring, including post-mortem examinations, while £2.3 million was spent on assessing efficacy.
An independent expert panel concluded that "controlled shooting" of free-running badgers was not effective or humane, and wildlife campaigners have raised concerns that monitoring by the panel has not resumed for the second year of the cull.
Anti-cull campaigners also said the figures did not include the costs of policing, which they said were £3.5 million - bringing the total cost for each badger killed to more than £5,200.
Ministers and farmers insist culling is necessary to address tuberculosis in livestock, which can catch the disease from badgers, with more than 26,000 cattle slaughtered in England last year and multimillion-pound losses.
The Government said every outbreak of TB costs £34,000, of which £20,000 is borne by the taxpayer.
But opponents say badger-culling is inhumane and ineffective, and alternatives such as vaccination should be pursued.
Dominic Dyer, of the Badger Trust and Care for the Wild, said: "If every badger killed last year cost the taxpayer £3,000, that would be a horrendous waste of money on a policy that leading scientists say won't work.
"But the reality is that every badger killed actually cost £5,200 - and that is simply beyond belief.
"The Government claim they have to do something as bovine TB costs the country a lot of money, and they say that 'doing nothing is not an option'.
"But just over the border in Wales, they have looked at the problem, thoroughly tested their cattle so they really understand how many actually have the illness, and brought in more frequent testing and better movement controls.
"By doing that, they have brought down the number of cattle slaughtered for bTB by 48% in five years.
"England has a policy that is inhumane, unscientific and is throwing money down the drain."
A spokeswoman for the Environment Department (Defra) said: "England has the highest incidence of bovine TB in Europe.
"The cost of the badger culls needs to be seen in the context of the devastating scale of the threat bovine TB poses to our farming industry and food security - £500 million over the last decade. Doing nothing is not an option.
"We are pursuing a comprehensive strategy, including tighter cattle movement controls, badger vaccination and culling.
"Many of the costs associated with the pilot culls last year were one-offs and have not been repeated this year."
Shadow environment secretary Maria Eagle said: "The Tories have failed to explain why they're pressing ahead with badger culls which have been shown to be ineffective, inhumane and now these figures also reveal that they are at huge cost to the taxpayer.
"It is appalling that the Tory-led Government has spent millions on scientific evidence that they've now chosen to ignore. The culls have already been shown to be an epic failure and they should be abandoned."
National Farmers' Union president Meurig Raymond said: "We are committed to trying to tackle this disease on all fronts - and vaccination of badgers may have a role to play in areas of the country which are currently TB- free.
"As well as slaughtering any cattle which are infected with TB, farmers are also increasingly controlling the movements of cattle to prevent the spread of disease further.
"However, the disease is endemic in badgers in some areas of the country and therefore it's vital that this route of infection is also contained if we are ever going to get TB-free.
"Therefore it remains hugely important to see the two pilot badger cull areas rolled out to other areas where TB is endemic - and as soon as possible."
Figures from Defra show that the Government has paid out £314 million in compensation for cattle slaughtered because of TB controls between 2002 and 2013 - around £1,180 per animal on average.