The pluvial mist of English July wraps Warren Farm in the Mendip Hills, as James Small prepares for a morning testing his cattle for TB. His beef herd is under "restriction" after two cows showed signs suggesting bovine tuberculosis, or bTB. One was cleared, the other had to be destroyed.

"We're an annual testing parish," explains Small, who will wait a statutory 60 days for a further round of tests. "If we go clear, we'll have the restrictions lifted and can resume business. But 60 days is a long time in any business." He adds: "We're a closed herd. Wherever it came from, it wasn't from other cattle. I'm not saying I know it was a badger, but it can only have come from wildlife."

England is now in limbo over an issue that arouses extreme passions in the countryside. A proposed cull of badgers in two pilot areas – one just west of here in Coleridge country, the Quantocks; the other in Gloucestershire – was launched by the Department for Environment, Food and Rural Affairs, to be licensed to private marksmen by Natural England. But it was halted by the Badger Trust, which secured a judicial review, heard at the end of last month.

Mr Justice Ouseley must now decide whether to open the way to the killing of tens of thousands of badgers in pursuit of reducing bTB, or to rule the killing unlawful on the grounds that it would cause the spread of disease and would be based on a flawed cost-benefit analysis and guidance to Natural England, which Defra had no power to make. He is expected to rule within weeks.

Wales faced a similar judicial review and abandoned the cull as unlawful in favour of badger vaccination. Scotland, which is decreed bTB-free, does not cull its much lower population of badgers. The National Farmers Union insists that culling is the only way to reduce, let alone eradicate, bTB, while the trust argues that, according to science and experience, it causes unnecessary slaughter and spreads the disease.

James Small is Somerset county chairman of the NFU and speaks for dairy as well as livestock farmers who raise cattle for beef. "Beef prices are up, so is our turnover, but also the expenditure that offsets our income – diesel, fertiliser. The dairy farmers are at the edge. It takes a certain character to be a dairy farmer, but some are thinking, as TB becomes yet another problem, 'Why am I bothering to do this?' And you can't just switch to arable, because this is the south-west, the land is like this" – he slants his forearm over a box of biscuits in the farm kitchen – "and it pisses down. We have a strong environmental sensibility in this country," he observes, "and that's fine. But it gets very Enid Blytonish, you know – lovely badgers. But this is not about badgers. It's about getting rid of TB."

Opposition to the cull is based on the premise that it will not work. High above the Somerset Levels on the edge of the Mendips, with a breathtaking view of Glastonbury Tor, Adrian Coward talks about his work as an ecologist working in the countryside, often with farmers, and his post as chairman of the Somerset Badger Group.

"Farmers say country people understand the countryside and city people are sentimental about wildlife. But I was born in the country and work in the country and I spend much of my time working with farmers who want nothing to do with the cull on their land. It is understandable that farmers are desperate to resolve this terrible disease, but killing badgers is not the solution."

Coward challenges the efficacy of a cull that, on its supporters' best estimates, could eliminate 16% of the disease over nine years. "If we had to make a business decision based on a 16% profit and an 84% loss," he says, "we'd be more concerned about the 84% loss! There is a false premise to the whole badger element of this thing."

Farmers are coy about putting their names to what they have to say about badgers. Some in the cull zone, like a man taking a break at the Bear Inn at Wiveliscombe on its edge, say they are anxious to enrol in the cull, but terrified of protesters based in Bristol. Among Coward's farming contacts is a man who talked about "considerable pressures from the NFU to sign up for the cull, told that if they don't, they're irresponsibly harbouring the disease".

The European badger, Meles meles, has a special place in natural lore – adored and reviled. In Celtic tradition, it is mystically associated with the full moon and tens of thousands of people belong or affiliate to the Badger Trust. The badger is a sympathetic recluse in The Wind in the Willows, but darkly sinister in Beatrix Potter – and, infamously, baited for sport.

Those who understand them do so well, like one of Coward's group, a former RAF flight sergeant and avionics technician, who didn't want to be named. He now lives in Glastonbury, volunteers at the Secret World animal rescue centre nearby and is on call day and night to deal with sick and injured badgers.

"The farmers and the other side are always calling us bunny-huggers," he says, "but we're not. We're committed to wildlife, yes, but I've had to arrange for plenty of badgers to be put down. I've been working with badgers for so long I'm sick of hearing the arguments: the simple fact is that, although badgers do cause TB, so do other cattle as they move around the country, often with their ear tags taken off and replaced to avoid the controls. The badger is the scapegoat."

Ouseley is faced with the argument that science, not sentimentality, vindicates the flight sergeant's view. Among the Badger Trust's key witnesses was a world expert on badgers, Dr Rosie Woodroffe, who commutes between her home above Mount's Bay in Cornwall and her job at London Zoo.

She argues that the transmission of bTB is "best viewed as a dynamic picture, with infection transmitted via four different routes: cattle-to-cattle, cattle-to-badger, badger-to-badger and badger-to-cattle… It is meaningless to refer to a certain constant proportion of cattle cases as 'coming from badgers'." Woodroffe was instrumental in previous major culling exercises between 1998 and 2005. She found that, although culling did reduce TB incidence in the culling area, it increased it in neighbouring areas "because of the way badgers – which are social and territorial and usually stay and live within the group they were born in – are disrupted. With their neighbours gone from adjoining areas, badgers range more widely, transmitting the disease to other badgers and more cattle herds." This phenomenon is known as the "perturbation effect". According to Woodroffe, "you end up with a greater risk to cattle than if you had done nothing".

Woodroffe is also uneasy about the new system for this cull: "free shooting" in open ground by teams of marksmen, which could result in injuries and appalling deaths for badgers that retreat to their setts to die. The government argues that "free-shooting" is cheaper than catching badgers in cages for killing, as was done under the previous culls.

As an alternative, vaccination of the kind that will now be undertaken in Wales, she says, "does not change the badgers' social structure. If you cull, the proportion of infected badgers goes up; if you vaccinate, it goes down."

More obviously sensible is to vaccinate cattle, "and our main recommendation is that there should be a cattle vaccine", says Woodroffe.

The NFU at national level disputes much of this. John Royle, the union's farm policy adviser, talks about "local creep" by TB at "the [geographical] edge of the disease which comes from wildlife. In terms of cattle measures, we're there – now we have a means to deal with the wildlife and accelerate towards eradication – so let's get on with it."

Above the Levels and Tor, Coward, placing his coffee cup back on a coaster with a badger on it, asks: "Why on earth cull or vaccinate wildlife to prevent the spread of disease among managed domestic stock? We all know that blaming badgers is the easy way out and that there's no long-term solution in killing badgers, but if the NFU gets its way, it will be too late."