Landowners have been condemned for shooting more than 1500 mountain hares this year in the Lammermuir Hills, southeast of Edinburgh.

Wildlife and animal rights groups say that the "mass slaughter" of a much-loved Scottish species is unjustified and cruel. But landowners insist the cull is necessary to protect grouse from disease so that they can be shot for sport.

The Royal Society for the Protection of Birds (RSPB) has received evidence that between 1500 and 1700 mountain hares were shot by landowners across the Lammermuirs in the spring. The figures are privately confirmed by landowners as "not unrealistic".

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Several sporting estates were involved in the cull, including Burncastle, the 8000-acre grouse moor near Lauder in the Borders owned by Ralph Percy, the 12th Duke of Northumberland. Based at Alnwick Castle in Northumberland, he has been listed by Country Life magazine as one of the UK's top 10 aristocratic landowners.

"Most people will be unable to see any justification for killing an iconic species, known to be in decline, on such an industrial scale," said Libby Anderson, policy director at OneKind, an Edinburgh-based animal welfare group. "This goes far beyond hunting for the pot or what some may call sport - it looks more like extermination. Killing in springtime is likely to involve the deaths of pregnant or lactating females, adding to the toll of suffering."

The large-scale culling of mountain hares is not illegal, though they are a protected species. Thousands are shot and trapped on uplands because land managers say ticks they carry spread a viral disease - louping ill - which can be fatal to grouse.

But a 2010 study by scientists at the former Macaulay Land Use Research Institute in Aberdeen and the University of Glasgow, which has been seized on by opponents, found that killing hares is not an effective way to control the disease.

Jonny Hughes, chief executive of the Scottish Wildlife Trust, described the "slaughter in the Lammermuirs" as another blow to Scotland's poor record on wildlife protection. "We strongly condemn the wholly unnecessary persecution of these iconic mammals," he said. "We urgently need a national monitoring programme for mountain hares so any control that may be required is based on science, and only goes ahead as a measure of last resort."

Duncan Orr-Ewing, head of species and land management at RSPB Scotland, argued mountain hare culls were unsustainable, and the science behind them thin. "Any reduction of mountain hares in the south of their range is of particular conservation concern as these are isolated populations, which are declining," he said. "We are calling on the Scottish Government to better regulate driven grouse shooting and introduce a system of licensing conditional on compliance with the law and best practice."

The issue is now going to be raised in Holyrood by the Green MSP for Lothian, Alison Johnstone. "To hear reports of mass culls is deeply disturbing," she told the Sunday Herald. "The commercial nature of large sporting estates must not be allowed to trample over the conservation of highly valued wildlife."

A spokeswoman for the Duke of Northumberland confirmed that there had been a hare shoot on his estate in the Lammermuirs this year. "This was routine, carried out to control numbers and hence maintain balance within the fragile uplands habitat," she said. "The bag was not exceptional, with all of the game sold to the local game dealer."

Tim Baynes, director of the Moorland Group of the landowning organisation, Scottish Land & Estates, was critical of the RSPB raising concerns. "Mountain hares breed very successfully in areas such as the Lammermuirs because grouse moors manage the habitat and control foxes and stoats which will predate young hares," he said.

"However, breeding success brings its own problems because mountain hares are a vector for the sheep tick which carries diseases such as louping ill. Therefore, their numbers are sustainably managed with culls."

The Scottish Government, however, said it didn't believe the risk of disease justified the "large-scale removal of mountain hares". A spokeswoman added: "We do have concerns about the intensification of management on some driven grouse moors."

Wildlife agency Scottish Natural Heritage stressed that mountain hares must be managed sustainably. Because of concerns of "possible over-exploitation", the issue was under review by experts due to report in December.