In 2012 alone, special permission was given for nearly 2,000 of the animals to be killed at times of the year when the practice is usually illegal.
The information was supplied by government nature agency Scottish Natural Heritage (SNH) under a freedom of information request from the Scottish Gamekeepers Association (SGA).
It shows that all licences allowing native mountain hares and brown hares to be culled outside the legal shooting season were granted to prevent “serious damage to livestock, foodstuffs for livestock, crops, vegetables, fruit, growing timber, fisheries or inland waters”.
Most of the UK’s mountain hares, which are indigenous to the Highlands, are found in upland areas north of the Border. But research suggests numbers have declined by around 43 per cent since 1995.
The Wildlife and Natural Environment Act, which came into force in 2012, introduced a closed season to protect hares at vulnerable times of the year.
It is illegal to kill them outside these times, except under licenses granted in “exceptional circumstances” by SNH.
These include situations where hares pose a threat to animals or crops through spread of disease or damage, and only if a cull will not impact on the conservation status of the species.
“We know mountain hare numbers in some areas of new woodland are having to be kept right down, all year round,” said SGA chairman Alex Hogg.
“With further ambitious targets for new tree-planting schemes in Scotland, the use of out of season licences to suppress the numbers to enable tree establishment is likely to become the norm.”
There is currently no monitoring of the number of hares that can be killed during the open season – which is from 1 October to 31 January for brown hares and 1 August to the end of February for mountain hares – but a SNH survey revealed that nearly 25,000 mountain hares were culled across 90 Scottish estates from 2006 to 2007.
The number killed is thought to represent 7 per cent of an estimated population of 350,000 across the UK.
Animal welfare activists have accused grouse shooting estates of mass slaughter and say culling should be outlawed at all times. Campaigners are staging a protest outside Holyrood next week to call for a ban.
“Whatever the excuse, we believe that the indiscriminate culling of mountain hares is unjustified and inexcusable,” said Harry Huyton, director of Scottish group OneKind.
“Most of these culls take place during the open season. These culls are unregulated and not monitored in any way.”
Robbie Kernahan, head of national operations for SNH, said: “We’re asking estates for restraint on large-scale culls of mountain hares.”