First licence expected to be issued in policy that could lead to a third of the animal's national population being shot

The government is poised to give the go-ahead to the first full-scale cull of badgers in England, under a policy that could soon mean as many as 100,000 of the animals – a third of the national population – are shot dead by farmers in an attempt to protect cattle from bovine tuberculosis.

According to Whitehall sources, the first of two licences is expected to be issued as soon as Monday for a large pilot cull area in Gloucestershire, which is a hotspot for bovine TB.

Previously, there have been localised trials to test the science behind such culls. Yet despite the mixed results of the tests, ministers have decided to push ahead with the national scheme after winning an appeal-court battle brought by campaigners last week.

In 2011, 26,000 cows were slaughtered because of the disease, which can also be carried by badgers.

A decade-long scientific trial of badger culling concluded that such killing could make "no meaningful contribution", and was "not an effective way" to control the disease. But the government is going forward with the plan under intense pressure from British farmers.

A Defra spokesman said: "We will continue to work with the farming industry so badger control in two pilot areas can start as soon as is practical."

As yet, no badgers have been killed as part of the cull, but with only straightforward administrative steps required after the granting of the licence, culling could begin within days.

Owen Paterson, the environment secretary, is a fervent supporter of the cull, having tabled a record 600 parliamentary questions on the issue while serving as environment spokesman in opposition.

In an interview with the Farmers Guardian on Friday, Patterson appeared to cast the proposed cull as being of benefit to badgers: "I find the attitude of those who want these wonderful animals to die of this disgusting disease [bovine TB] completely incomprehensible."

But Mary Creagh, the shadow environment secretary, said: "The cull will cost more than it saves, put a huge strain on the police, and will spread bovine TB in the short term as badgers are disturbed by the shooting. Ministers should listen to the scientists and can this cull – which is bad for farmers, bad for taxpayers and bad for wildlife."

A source in Paterson's department said the controversial policy was causing great anxiety: "The panic among senior officials outweighs anything since foot and mouth. It makes The Thick of It look tame and gentle."

The government has refused to release numerous documents under freedom of information rules, including advice from the government's chief scientific adviser, Sir John Beddington, and communication with the National Farmers Union. The latter was blocked on the grounds that it was "internal communication".

Natural England, the licensing body, said: "We are working flat out with licence applicants on processing their applications. We will issue licences to enable control activity to commence in the pilot areas as soon as is possible."

The licence will be issued to a group of farmers and landowners who will commit to killing at least 70% of the badgers on their land for at least four years in a row.

The government's own impact assessment concluded that it would cost farmers more to carry out the cull than to do nothing and suffer any losses from bovine TB.

The licence area must also have "hard boundaries", such as rivers, to prevent badgers fleeing and potentially spreading the disease and making the situation worse.

The government pointed to the 16% cut in bovine TB found at the end of the 10-year trial but the new culls will use a different killing method. Instead of trapping then shooting – considered expensive – the badgers will be "free shot" by marksmen. The deaths have to occur before 1 February, when the close season for badger shooting begins and runs till 31 May.

But the start of the cull could be halted by a legal challenge to the licence. The Badger Trust, which unsuccessfully challenged the government's cull policy in the appeal court last week, stated: "We will continue to pursue all legal means to stop culling. We will closely study any licences issued by Natural England." The trust was successful in a previous legal action against badger culling in Wales. Campaigners are also pursuing a complaint against the government in Europe under the Bern convention, which governs wildlife and habitat protection.

A licence for a cull in Somerset is thought to be taking longer to process due to a legal issue involving the crown estate, but sources said they did not expect that to prevent the licence being granted in due course.

Animal rights campaigners are determined to halt the trials through protests at the cull sites, whose location is not being made public. Volunteers plan to patrol the zones and stop the badgers coming into the open.

The Gloucestershire and Somerset culls are trials meant to test whether free shooting is as effective as trapping and shooting.

Critics say the short time of the trials will be insufficient for comparison with the decade-long trial, but if the government calls the trials a success, killing will happen across affected areas in England and is expected to end the lives of 70,000 to 105,000 badgers – from an entire UK population estimated at 300,000.

A badger vaccination plan is replacing the Welsh cull. Vaccination is also being tested in Devon by the National Trust, and by the Wildlife Trust in Gloucestershire.

The last Labour government said an oral badger vaccine would be ready by 2015. The coalition cancelled five of six trials of injectable vaccines, and said a viable oral vaccine was "years away".