The Government's plan to cull badgers could wipe out "entire clans" of the animals in their heartland in the South West, according to experts.
Natural England, the Government's own wildlife advisor, has warned that local extinctions "cannot be ruled out".
They fear that up to 79 per cent of badgers could be wiped out in cull areas – that is up to almost a third of the national population.
Officials have also told ministers that a cull also posed a "significant risk" of breaking European wildlife laws.
Animal rights groups are already challenging the controversial cull in the High Court but Environment Secretary Caroline Spelman insists something must be done to tackle the menace of bovine tuberculosis, which is on the rise.
The shooting of up to 130,000 badgers is intended to curb the condition, which led to the slaughter of 25,000 cattle in 2010 and cost taxpayers £90m.
But Natural England told ministers: "We have a low level of confidence that the predicted benefits (of the cull) can be delivered consistently."
Officials wrote: "Reducing the badger population on the scale permitted under this policy has not previously been sanctioned for any protected native mammal species in modern times."
The newly-revealed documents constitute official advice given by Natural England to Mrs Spelman and were released under freedom of information rules to Labour's shadow environment secretary, Mary Creagh.
She said: "Ministers have ignored scientists' advice that a cull will have a marginal effect on bovine TB. The scientists also confirm that the cull could spread TB in cattle if farmers fail to oversee an effective cull.
"Ministers should listen to the scientists and 'can' this cull, which is bad for farmers, bad for taxpayers and bad for wildlife." A spokesman for the Department for Environment, Food and Rural Affairs said: "Culling will only take place in the localised areas where it will make a difference, the number of licences will be limited, the licence will specify the maximum number of badgers that can be controlled, and the number of animals controlled will be monitored to guard against local disappearance."
In its advice, Natural England estimated the number of badgers that would be shot over the four-year culls at between 90,000 to 130,000. Its highest estimate of the proportion of badgers that this represented in the West and South West of England, was 79 per cent.
Its main "credible and objective" estimate for the regions was 25 to 54 per cent but that was not the "maximum extent" to which culling could occur, according to officials.
Its report said: "It is our view that the local disappearance of the badger in some areas cannot be ruled out."
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