The Government has sanctioned a cull of badgers in a bid to finally end the misery of tuberculosis in cattle blighting the Westcountry.

Environment Secretary Caroline Spelman announced in the Commons yesterday six-week "pilot" culls will take place in two areas in autumn next year.

Ministers will choose from a shortlist of potential cull areas to be drawn up next month. Mrs Spelman said they would take place in areas devastated by the disease, namely the South West.

Devon or Cornwall and Gloucestershire are thought to be the front-runners.

If the pilots are effective, they would clear the path for up to 40 culls in "hotspots" as part of a package of measures to eradicate the disease.

After 15 years of fierce debate, farming leaders hailed the decision to tackle bovine tuberculosis (TB), which led to nearly 25,000 cattle being slaughtered in England last year.

But animal welfare groups are horrified, and police forces could be saddled with a £500,000 a year bill to keep the peace in each cull area.

Mrs Spelman told MPs: "I am acutely aware that many people are opposed to the culling of badgers and I wish that there was a current satisfactory alternative.

"But we can't escape the fact that the evidence supports the case for the controlled reduction of the badger population in the areas affected by bovine TB."

Mrs Spelman insisted the decision to pilot culls, set against the disease potentially costing taxpayers £1 billion over 10 years, is based on science.

The pilots next year will determine whether "controlled shooting" – licensed deer-stalkers shooting free-running badgers – is safe, effective and humane.

While far less controversial, vaccines for badgers and cattle are fraught with difficulties, ranging from high costs to being years away from approval.

On Monday, the Western Morning News reported the minister would give the pilots the go-ahead, but that they would have to wait until after the Olympics against fears police forces would be over-stretched. The autumn start also gives ministers chance to ward off an "inevitable" legal challenge. The Badger Trust said it was "clearly very disappointed" and would consult lawyers to decide what action could be taken.

For the pilots to be successful, the badger population will have to be reduced by 70 per cent in each area, leading to a possible reduction of bovine TB by 16 per cent.

Yesterday's announcement was "another massive step forward", said the National Farmers' Union. In July, Mrs Spelman said she was only "strongly minded" to authorise culling.

In the Commons, Neil Parish, Conservative MP for Tiverton and Honiton, who sits on the environment select committee, said the decision was "absolutely right".

He said: "If you tackle the disease in the wildlife, you stop it reinfecting the cattle every year, which is what has been happening for years. The only way they tackled the disease in New Zealand and Australia was by tackling it in wildlife."

But Andrew George, MP for St Ives and Lib Dem agricultural spokesman, said: "We must all hope that this policy will help and not make the matter worse. In particular the Government will have to strengthen its plans to undertake a proper and rigorous assessment of the badger population in each of the pilot areas."

Mary Creagh, Labour's Shadow Environment Secretary, said: "The cull will cost farmers more than it saves them and will spread bovine TB in the short term as badgers move out of cull areas. This is bad news for wildlife, farmers and the taxpayer."