Trial badger culling in the Westcountry will be the most contentious issue in farming this year, with the plans coming under increasing pressure. Farming Editor Peter Hall reports.

It was always going to be a toe-in-the-water experience, a trial to sort out the semantics of killing wild badgers to stop the onward progress of bovine tuberculosis.

This appalling disease causes the deaths of up to 40,000 cattle a year, utter anguish to the farming community, and an enormous bill to the public purse.

News, last month, that the go-ahead had been given by the Government for two pilot culls next year – one almost certainly in the Westcountry – was greeted with only muted enthusiasm from the agriculture industry, and with predictable censure from animal-welfare organisations.

But a general feeling of "too little, too late" pervaded the announcement, and since then the dissent has grown, with farming organisations voicing a range of concerns about the delivery of the culls, chiefly the security of the vets and workers carrying out the trials and the farmers on whose land the culls will be held.

Make no mistake, while responsible environmental bodies like the Badger Trust insist their members will obey the law and limit their activities to legal protest and challenges through the courts, there are animal-rights extremists who will be prepared to take drastic and violent action. This is not media hype; why else have the pilots been ordered after the London Olympic Games are over, when there will be sufficient police numbers to cope with warfare in the countryside?

The pilot culls are the best deal the farming industry is going to get, worked out after months of detailed planning. If successful, they could lead to a vastly larger campaign.

That has been the attitude of most of the professional farming organisations: at least give it a chance, then we can fine-tune it.

Projections that a third of the badger population could be destroyed in the long term appear inflammatory and far-fetched in the extreme. But the past few weeks have seen growing concerns among the farmers.

As matters stand, ministers will choose from a shortlist of potential cull areas some time this month. All badgers in 70 per cent of the pilot area would be culled by shooting, either running free or trapped first, leading to a possible reduction of bovine TB by 16 per cent. The experiment would last for just six weeks.

But responsibility for issuing culling licences to organised groups of farmers, formed into companies and working under supervision of vets, has been vested in the Government's own environmental organisation, Natural England, rather than its veterinary organisation Animal Health, which was what the farming industry would have liked. While this could be seen as a move to keep its environmentalists on board and involved, the administration is taking a calculated risk.

Natural England could leak like a sieve, with detailed information about where and when culls were to be held all too readily available.

And Natural England has stated it will give the public an opportunity to comment on the licence applications – a strategy labelled as "bureaucracy gone mad" by Cornish beef farmer Bill Harper, chairman of the National Beef Association's TB committee. Anonymity of those involved was vital, he said – and the maps used in the consultations should not be too precise.

But he was confident the campaign could work. He told me: "When the full scheme is rolled out in 2013 it will really start to have an effect on reducing the dreadful TB problem."

Many farmers believe a different approach should be taken. Instead of culling healthy badgers along with infected ones, the focus should be solely on diseased animals.

There are specialists who have studied badgers for years – men like Bryan Hill from Okehampton – who can identify diseased setts. But generally they do not have the academic qualifications deemed necessary to do the job ... which is a very great pity.

If a cull based on taking out only diseased animals were allowed, the whole business would be a very great deal more palatable and acceptable to a public that is largely urban, and bases its concept of badgers on kindly characters from Beatrix Potter and The Wind in the Willows.

It would also make it a great deal more difficult for the pro-badger lobby not to get involved in a united campaign for healthy animals, both wild and domestic.

In the long term, we can look forward to the development of TB vaccines for badgers and cattle, plus (and here's the pipe-dream) a reworking of the Badger Act to establish a properly managed, limited population, disease-free and able to feed itself adequately, thus also resulting in more ground-nesting birds and hedgehogs.

But in the short term it could be tin-hat time in the rural Westcountry next autumn.