The Badger Trust has threatened a legal challenge in a bid to stop the forthcoming badger cull trials in two South West areas.

The organisation has written to the Department for Environment, Food and Rural Affairs giving it notice of the grounds of challenge, which it intends to pursue if the Government presses ahead with the pilot culls as part of its campaign to stamp out bovine tuberculosis.

Defra has until Friday of next week to respond before the trust begins proceedings, but both the Government and farming organisations are expecting a legal challenge.

Last month a decision was taken to allow pilot culls in a TB hotspot area of West Somerset and another in West Gloucestershire. Marksmen from licensed groups of farmers would cull badgers on at least 70 per cent of land in the areas, monitored by a panel of experts from the Royal Veterinary College.

In its letter, the Badger Trust says it believes the policy could be unlawful, giving three grounds on which it bases the claim.

The cull, as proposed, would not meet the "strict legal test" of "preventing the spread of disease" in the licensed areas and could, indeed, actually spread the disease, it said.

It claimed that the guidance on culling given by the Government to Natural England, the licensing body, was invalid, and stated: "Killing badgers is not in fact one of Natural England's functions, which are mainly focused on maintaining biodiversity."

And the trust also challenges the plans on cost issues, arguing that Defra's assessment was based on the free-shooting of badgers, a method "assumed to be much cheaper" than cage trapping.

It states: "If, after the first year of piloting the plans, free-shooting is ruled out for being inhumane, ineffective or unsafe, farmers will be legally obliged to continue the cull on a much more costly trap-and-shoot basis."

This meant significant financial risks for farmers, not properly reflected in the cost impact assessment which underpinned Defra's decision. "This may render the decision unlawful," it adds.

The Badger Trust said it had written the letter, and its deadline for a reply, after taking extensive legal advice, as well as holding several discussions with ministers in person.

Badger Trust chairman David Williams said: "The Badger Trust has responded in detail to both Defra's consultation papers on culling, and suggested viable alternatives.

"However, our concerns that the culls proposed will actually spread the disease have not been heeded. In the light of this, and our concerns over the legality of the decision, we would be failing in our duty to badgers if we did not pursue a legal challenge, despite the difficulty and cost risks involved.

"If there is an opportunity to save many thousands of healthy badgers, as there is here, we must take it, on behalf of the many local badger groups and supporters on whose behalf the Badger Trust works. If successful it would also save farmers the expense of a policy which would not benefit them."

The farming industry has been resigned to facing a legal challenge since the cull announcement – earmarked for this summer and autumn – was made.

"News that the Badger Trust has taken the first steps towards a legal challenge is not surprising," said Mel Squires, South West regional director of the National Farmers' Union. "But we remain committed to supporting the Government's TB-eradication policy to tackle this terrible disease.

"We hope the process is swift and resolves any issues as soon as possible."

Bovine TB was responsible for the deaths of 25,000 cattle in England last year. But both Labour and the RSPCA oppose the current cull plans, clearly the most contentious issue currently facing farming.