Consultation has just closed on plans to define parts of the country as wild land, as detailed by Scottish Natural Heritage on a map setting out 43 areas of rugged, remote and challenging terrain, the majority of which are in the Highlands and Islands.
However, the body representing local communities that own more than half a million acres of land such as Assynt, Eigg, Knoydart and Gigha said officials must not do anything to prevent their deserted and ruined settlements eventually being repopulated.
Community Land Scotland urged SNH to acknowledge that, until relatively recently, people used to live on what is now seen as wild land and the present human deserts are man-made.
Any resulting map should be overlaid by one which records those who were cleared, it said.
In its submission to SNH, the umbrella organisation for community landlords said the wild land areas mapped have a significant overlap with the "fragile areas" of Scotland.
It added: "The map also overlaps with many areas purposefully and shamefully cleared by past generations of landowners.
"It is these actions to clear land which have given rise, in part, to any sense that such land is now uninhabited and often relatively inaccessible countryside where the influence of human activity on the character and quality of the environment has been minimal'."
Community Land Scotland said the reason some of the areas were uninhabited was past actions by landowners and the wild land map should not impede the aspirations of local people for economic and social development, or those who may market their area through the concept of wild land.
David Cameron, Community Land Scotland's chairman, said the organisation was not against the mapping.
However, he added: "It has to be very carefully looked at, and using a map alone is a blunt instrument which disregards so much human history."
The Core Wild Land 2013 Map was published earlier this year by SNH.
It is designed to inform planners and political decision makers on which areas are considered the most environmentally valued and important. SNH stressed it would not constitute an environmental designation but was a strategic tool for use in planning policy.
Others have welcomed it as a way of as a way of preventing the likes of large scale wind farms in areas with little or no habitation.
However, Highland communities are concerned it will obstruct vital local development.
The community-led Storas Uibhist, which owns the bulk of the islands of Benbecula, Eriskay and South Uist, has already made it clear it fears a wild land designation could set back its attempts to stem the tide of depopulation.
SNH's Simon Brooks, who has been managing the wild land consultation, said the organisation welcomed "the thorough submission" from CLS and would consider it in preparing the agency's consultation report to Government.
He added: "We recognise that virtually all of Scotland has been influenced by human activity in some form or other over time, but many areas continue to have strong qualities of wildness that are highly valued today.
"Our map of core areas of wild land identifies the largest areas where the experience of wildness is strongest, and is intended to inform decisions on how best to manage what is clearly an important economic asset to Scotland."