When journalists were summoned to a stuffy room in Whitehall to hear Defra's scientists explain why a cull of badgers was a necessary step to combat bovine TB in cattle, we were given a formidable array of statistics. There were 3,622 new outbreaks of TB in cattle in 2010, a 7.5% increase on the previous year, leading to the slaughter of 25,000 cattle. Over the next decade, TB in cattle is projected to cost £1bn. Nearly one in four cattle farms in the south-west is currently restricted (farmers are not free to sell or move their cattle) because of the disease.

Behind these figures is genuine misery. Farmers have seen herds they have tended for generations destroyed. They are desperate for something to be done about badgers, which scientists agree are one way in which TB is transmitted.

Human misery verses the slaughter of one of Britain's best-loved animals has created a polarised debate. Our attachment to badgers may be irrational when we already cull plenty of wildlife, from deer to grey squirrels. But the proposed pilot cull is just as irrational. The mood of Defra's vets and scientists – one of "there is no alternative" – was reminiscent of the government's attitude before the Iraq war. Minds had already been made up and now the facts were being marshalled to support them.

The new pilot cull is not scientific. It is not randomised or replicated, there are no controls and no independent scientist at the helm, and the government has no clue if it will be effective.

The science has already happened. The randomised badger culling trial was a heroic, £56m, 10-year project, overseen by Sir John Bourne, a hugely respected scientist. After trapping and shooting in cages nearly 12,000 badgers, they found culling produced a net reduction of bovine TB in cattle of 16%.

So culling works, in a very limited way. As Professor Lord Krebs, who recommended the original cull trial, put it: this expensive process left nearly 85% of the problem still there.

The new pilot cull is different in one crucial respect: instead of being trapped in cages, there will be "controlled" shooting: badgers will be lured to feeding stations at night where professional marksmen will bring them down.

This has never been done before. At best, its effectiveness is unproven. At worst, scientists say it is a recipe for "perturbation". Chris Cheeseman, an eminent former government scientist, has studied badgers for four decades and worked on the 10-year cull. He is also an expert marksman and, in the days when it was legal, shot badgers. Even multiple shooters firing simultaneously at a group of badgers will never kill them all, he says. Those that aren't maimed will escape. Badgers live in social groups. When these are disrupted, they abandon their setts and seek new territories – spreading disease. It would be impossible to design a better way of causing perturbation than by shooting.

Why shoot badgers in this way? Money. Defra costs cage-trapping and shooting at £2,500 per sq km a year. "Controlled" shooting, it claims, would cost just £200 per sq km a year. The latter figure is certain to be an underestimate: policing the countryside when animal rights activists disrupt the nocturnal shooting of badgers is going to be hideously complicated – and expensive.

And there are alternatives. The National Trust and Gloucestershire Wildlife Trust are already vaccinating badgers against TB by trapping and injecting them. This is a "big society" solution, but it is too expensive to be used on every badger in the land.

An oral vaccine for badgers would be far cheaper because it could probably be scattered on the ground inside peanuts, every badger's favourite snack. Defra insists it is developing this, but there is no prospect of success before 2015. Here there seems to be a lack of political will – in New Zealand scientists have developed an oral vaccine to eradicate TB from its detested possum population.

Ultimately, stopping TB in cattle requires a vaccine not for badgers but for cows. The problem is distinguishing between a vaccinated cow and a cow with TB. Scientists are close to devising a reliable test to distinguish between the two, but Britain would then need to persuade the rest of the world to accept that we were selling them vaccinated cattle, not cattle with TB.

Until then, the smartest approach would be to learn to live with TB: to compensate farmers properly, to farm more disease-resistant cattle breeds and even give farmers incentives to diversify away from cattle in disease hotspots. Most radically of all, we could ask whether we really need to slaughter every cow carrying a disease that poses minimal risk to human beings.