The number of the creatures, native to the Highlands, being culled is not monitored and is unregulated during the open season.
Landowners say culls protect red grouse from tic-borne disease and prevent over-grazing.
Latest figures produced for the Scottish Government, but not published until now, have revealed killings average 25,961 a year and reached 37,681 in 2014.
The figures emerged after a joint statement with the shooting industry was issued by the Government promising “voluntary restraint” on large-scale culls.
First Minister Nicola Sturgeon condemned large-scale culling in March and said legislation and a licensing scheme were being considered.
Scottish Natural Heritage (SNH) has advised the Government it may have to report the mountain hare population was in “unfavourable status” to the European Commission.
Harry Huyton, director of animal welfare charity OneKind, claimed large-scale mountain hare shooting was routine and voluntary solutions were not working.
He said: “Scottish Natural Heritage should be leading the way when it comes to protecting wildlife, but instead it appears to be holding the Scottish Government back from taking action against unregulated mountain hare killing.
“Evidence of significant declines in mountain hares in parts of Scotland is being disregarded.”
Eileen Stuart, head of policy and advice at SNH, urged estates to “exercise caution”.
“While there is currently no evidence of a national decline in mountain hares, the surveillance scheme we are starting this winter will give us a better understanding of the distribution and abundance of mountain hares across Scotland.”
But Tim Baynes, director of the Scottish Moorland Group representing estate interests, said: “The data since 1954 provides no evidence for an underlying decline in the hare population and underlines the point, confirmed by SNH in its evidence to the [Holyrood] petitions committee in October 2017, that mountain hare populations move in cycles and so does the need for management of their numbers.”
The Scottish Government said it opposed “any level of culling threatening the conservation status of Scotland’s mountain hares” and was discussing the evidence and next steps with land managers as well as conservation bodies.