A “perfect storm” of intensive farming and rising badger populations has left most of the countryside in England and Wales devoid of hedgehogs, according to the first systematic national survey.

The research used footprints left by hedgehogs in special tunnels to reveal that they were living at just 20% of the 261 sites surveyed. Hedgehogs, which topped a vote in 2013 to nominate a national species for Britain, were significantly less common where badgers were more numerous. Badgers eat hedgehogs and also compete for the beetles and worms the prickly animals consume.

However, hedgehogs and badgers lived alongside each other in half the hedgehog sites, while a quarter of all the sites had neither animal, showing the destruction of habitat such as hedgerows and coppices was also a major factor.

“There are lots of areas in the countryside that are not suitable for hedgehogs or badgers,” said Ben Williams, at the University of Reading, who led the new work. “There is something fundamentally wrong in the rural landscape for those species and probably lots of other species as well,” such as birds and shrews.

Previous work based on visual sightings and roadkills indicated that the number of hedgehogs living in the British countryside has plummeted by more than half since 2000. Historical hedgehog numbers are hard to estimate, but scientists think populations have fallen by at least 80% since the 1950s.

The new survey, published in the journal Scientific Reports, is much more detailed and reliable. It concludes: “The combined effects of increasing badger abundance and intensive agriculture may have provided a perfect storm for hedgehogs in rural Britain, leading to worryingly low levels of occupancy over large [areas].”

The scientists found no rural hedgehogs at all in the south-west of England. The animals are known to live in suburban areas in the region, but these are isolated and at risk. “If we get lots of winter flooding, during hibernation, you potentially wipe out a large area of hedgehog population, and if there is not a local population that can repopulate the area, you get an area that is desolate,” Williams said.

Badger numbers have roughly doubled since 1992, when they gained increased legal protection, although the population is probably still lower than in the historical past. But the new data suggests that badger numbers would have to rise sixfold from current levels to wipe out hedgehogs completely. “Badgers and hedgehogs can, and do, coexist, as was the case historically for thousands of years,” said Williams.

Hugh Warwick, at the British Hedgehog Preservation Society, said the research showed the value of back gardens as a refuge: “This fascinating piece of research reminds us of how vital a habitat our back gardens can be and one we can easily improve with a few small actions. The most important is to ensure that hedgehogs can get into your garden, and a small hole – 13cm – will do.”

There's a way to save hedgehogs – and all of us can help | Hugh Warwick Read more

While the intensification of agriculture since the 1950s has seen much habitat destroyed, more than 30,000km of hedgerows have been planted or restored in the last 20 years, according to the National Farmers’ Union. Pesticide use, which can kill the invertebrates that hedgehogs and badgers feed on, has been declining since 1990, the NFU says.

Williams welcomed these changes, but said it could take 20 years or more before they led to an increase in mature, valuable habitat: “It is likely we are not seeing some of the benefit of these changes immediately.”

He added: “However, I think there is a wider societal issue. Farmers get quite a raw deal and are blamed for lots of the habitat loss, whereas as a society we have decided we want lots of fairly cheap food and and we are not prepared to pay a premium for food that is farmed in a more environmentally way. As a society, we have to choose if we are prepared to pay that premium so we can have food alongside the benefit of a good environment.”