Mountain hares are facing extinction in large parts of the Scottish Highlands because landowners are killing thousands of them every year in order to protect the grouse shooting industry, wildlife experts have warned.

The distinctive mammals are being shot and snared by gamekeepers on grouse moors due to fears that ticks carried by hares spread a viral disease, which can be fatal to grouse. However, experts have poured doubt on claims that killing hares protects grouse.

"A preventable catastrophe has befallen the mountain hare," said Dr Adam Watson, a veteran mountain ecologist. "This is a national scandal."

Watson has just published a new book on mammals in the northeast Highlands in which he exposes the plight of the mountain hare. He has found "massive declines" over the last 10 to 20 years on grouse moors around Deeside.

"I would say that spring abundance of adults has been reduced by at least five-fold to 100-fold on most of these moors," he said.

In some areas, he said, hares have been completely wiped out, adding: "Gamekeepers on several estates have told me they were instructed to reduce hare numbers and to try to eradicate them."

Watson condemned the Government's wildlife conservation agency, Scottish Natural Heritage (SNH), for failing to protect mountain hares under European law.

He said: "SNH has known what has been happening for years and has done nothing about it. This is supine behaviour, pleasing to or subservient to powerful grouse-shooting interests, but wholly against the wider public interest."

Roy Dennis, who founded the Highland Foundation for Wildlife, said: "Numbers are drastically down. The decline is very noticeable over the last 20 years on intensely managed grouse moors. I think it's dreadful. There's far too much killing of mountain hares."

Claims that diseases carried by hares are endangering grouse are disputed. A study by scientists from the former Macaulay Land Use Research Institute in Aberdeen and the University of Glasgow in 2010 concluded: "There is no compelling evidence base to suggest culling mountain hares might increase red grouse densities."

The RSPB in Scotland called on SNH to take urgent action to help protect the mountain hare. The charity's Duncan Orr-Ewing said: "[The hare] appears to be suffering as a consequence of increasingly unsustainable and intensive management of huge swathes of upland Scotland with the sole intention of delivering very large bags of grouse for sport shooting."

SNH accepted that there could have been "localised extinctions" of mountain hares, and expressed concern about their "possible decline". A closed season was introduced in 2011 to limit the numbers shot during the breeding season between March and July.

The agency's Rob Raynor said: "We don't support large, indiscriminate culls of mountain hares and advise moorland managers to talk to us if they are thinking of culling hares in large numbers."

He said he was aware of allegations that some estates tried to eradicate mountain hares in an attempt to get rid of golden eagles, adding: "SNH condemns any systematic attempt to reduce hare numbers for this reason … it demonstrates no understanding of the ecology of predators such as eagles. If mountain hares become scarce or absent, the predator will switch increasingly to other more available prey, such as red grouse."

The most recent survey for SNH found more than 24,500 mountain hares were shot or snared by 90 sporting estates in 2006-07. Half were killed to try and control a viral illness known as louping ill, 40% were shot for sport and 10% for forestry or crop protection.

However, landowners have claimed evidence shows Scotland's mountain hare population to be "stable and robust". A 2007 survey suggested that the animals were present on 64% of the area of driven grouse moors.

Tim Baynes, of industry body Scottish Land & Estates, said: "The relatively high numbers on managed moors means that culling will not endanger the population."

Although thousands of mountain hares are killed every year, this is less than 10% of the population, he argued.

Alex Hogg, chairman of the Scottish Gamekeepers' Association, said that, because of the dangers of louping ill, which can infect humans, land managers had no alternative but to "suppress" the numbers of mountain hares on grouse moors.

Such arguments gave conservation groups little comfort. The volunteer-run Hare Preservation Trust is convinced hares are being killed in breach of European law.

"We have information that they are being wiped out on some estates," said the trust's John Rimington. "I don't think gamekeepers give two hoots about them."