Michael Eavis, the founder of Glastonbury festival and the best-known dairy farmer in Britain, has spoken in support of the badger cull.

The Somerset farmer, who keeps 400 dairy cows and has a badger sett at Worthy Farm, said he was "not inviting" gunmen to kill his badgers but he was in favour of the cull "in certain circumstances" when there is "a heavy loss of dairy cattle".

"As a dairy farmer I am not on the side of the badger," he told the Guardian, in his first public comments on the controversy over badgers' role in causing bovine TB in cattle. "They've also uprooted all the orchids, and killed or eaten all the hedgehogs. They're still treated like a protected species, but they're actually quite a damaging animal."

While Eavis's cows have never contracted TB, the 77-year-old farmer, who hosts the Rolling Stones for the first time when the 31st festival starts next week, highlighted the plight of a neighbour whose family business has been decimated by the disease.

"My first love apart from my wife and children are the dairy cows, because we've been doing dairy cows at Worthy Farm for 150 years," said Eavis. "If I thought for a moment badgers would infect my cows I know which side I'd be on. There's a farm three miles down the road that lost 500 cows to TB. That's the whole of his career, and his father before him, and his grandfather, just destroyed in one fell swoop. It is serious, I'm telling you."

Jeff Hayden of the Badger Trust called Eavis's comments about badgers and hedgehogs "ludicrous" and offered to vaccinate the badgers living on Worthy Farm so they would not have to be shot in a cull. The Badger Trust and other wildlife charities are providing a free badger vaccination service for landowners but most farmers are still in favour of the cull, which they believe will be more effective.

While the Glastonbury festival site is not in either of the first two zones where marksmen will begin shooting badgers this summer, it could fall within a future zone with the environment secretary, Owen Patterson, planning to widen the cull to at least 40 areas in the next four years, mostly in the West Country where the disease is particularly prevalent.

Hayden said Eavis was wrong to assume that killing badgers would solve the problem of cattle TB in these hotspots. "The scientific view is that a badger cull will only achieve between 12-16% decrease in the increase of TB in cattle after nine-and-a-half-years," he said. "Farmers ought to be putting pressure on the government to get a better TB test for cattle and expedite the TB vaccine for cattle."

Hugh Warwick, a hedgehog ecologist, said that Eavis was mistaken in believing that badgers were responsible for the loss of hedgehogs in the countryside.

"Hedgehogs and badgers have coexisted for millennia. When there is plenty of food for both, these animals can live together," said Warwick. "The reason we're seeing a decline in hedgehogs cannot be wholly blamed on badgers although badgers have some part to play in it."

Badgers and hedgehogs compete for the same food – worms – but when food is scarce, badgers will turn on hedgehogs. Hedgehogs do suffer if badger populations reach a certain density but they are also rapidly declining in areas where there are no badgers.

Adam Quinney, vice president of the National Farmers' Union, welcomed Eavis's comments and said they were typical of the vast majority of farmers.

"Sadly this has become a polarised debate and I applaud Michael for putting his head above the parapet when he didn't need to," he said. "Michael has tremendous support for what he's done around the Glastonbury festival and I hope people who go there realise he is a dairy farmer and has spoken from the heart on the subject. I hope they take that on board."