The policy of killing large numbers of Japanese sika deer has been agreed by the Forestry Commission, the Deer Commission for Scotland (DCS) and Scottish National Heritage amid fears that red deer could be wiped out within 50 years.
Under a plan backed by the Scottish Society for the Prevention of Cruelty to Animals, teams of marksmen will target the elusive sika deer, whose invasion of Europe has drawn comparisons with that of the North American grey squirrel.
The sika population constitutes a small but growing proportion of Scotland's total deer population and it is feared that cross-breeding between the two could do irreversible damage to the red deer's genetic integrity.
Dick Youngson, technical director of the DCS, said the aim of the cull was to preserve areas not yet touched by sika rather than to wipe the Japanese deer out completely.
He said yesterday: "It isn't going to be a mass slaughter. This will be a controlled attempt to manage - but not eliminate - sika. We don't want them colonising new areas and we don't want them causing damage to woodlands.
"Hybridisation has happened in many areas of Scotland, but there are parts of the country where it hasn't occurred. To preserve the genetic form of red deer as we know them, we want to separate these areas."
There are plans to make island sanctuaries for red deer in the Hebrides, on Harris and Lewis, North and South Uist, Rum, Arran, Islay and Jura.
The sika, first brought to Scotland in the 1890s, is detrimental to the forest industry and agricultural producers because of the harmful effects of its browsing, bark-stripping and grazing.
The Japanese deer breeds much more quickly than red deer because calves reach sexual maturity at an earlier age than their native counterparts. They also breed all year round.
The DCS says there is very strong evidence of crossbreeding in parts of Scotland, and points to the southern part of the Lake District and Co Wicklow, in Ireland, where there are now no "pure" red deer left.
The cull will not be easy. The deer's nocturnal nature and fondness for forest cover mean it can take hunters hours to find a single animal.