The eight-year research project by Forestry Commission Scotland indicates that over the past 40 years a significant amount of ancient woodland has been lost, up to 14% in some upland areas.
The Native Woodland Survey Of Scotland is believed to be the most comprehensive habitat survey project carried out in the UK and the first of its kind in Europe.
The voluntary approach to deer management is now being questioned and, while landowners and gamekeepers accept they face renewed calls for increased deer culls, they fear this would undermine the operation of important sporting estates.
It comes as the Scottish Parliament's Rural Affairs, Climate Change And Environment Committee prepares to publish a letter today to the Scottish Government on deer management, which is understood to contain "robust recommendations".
Speaking at the launch of the survey at Edinburgh Zoo, Scottish Environment Minister Paul Wheelhouse, said it had shown that 768,876 acres of Scotland's forests were native woodland.
But he added: "The findings suggest that over the past 40 years we have lost a significant amount of ancient woodland in the uplands, and the survey has shown the most widespread threat to native woodland health and regeneration is excessive browsing and grazing, mainly by deer."
He said much had been done over the past 30 years to reverse centuries of damage, with almost 20,000 acres of native trees planted. "Clearly, there is still much to do," he added.
Statutory responsibility for deer management lies with public body Scottish Natural Heritage, but voluntary Deer Management Groups have been established over the last 30 years to coordinate control of the animals between neighbouring landowners.
Richard Cooke, chairman of the Association Of Deer Management Groups, said the survey would be extremely helpful. He added: "We do believe, however, there has been a significant turnaround in the last 30 years in the impact of deer on native woodland and it is too easy to blame deer at every turn when other factors, for example grazing from other herbivores and now widespread tree disease, are also taking their toll."
He said it was clear effective deer management planning was vital, particularly at the early stages of any planting or regeneration programme. But he added that all available methods should be used, including deer fencing.
Alex Hogg, chairman of the Scottish Gamekeepers' Association, also called for fencing. Speaking about the survey, he said: "We fear the danger in this considerable piece of work is that conservationists will translate it as a green light to hammer Scotland's deer, which is not the long-term answer."
He said conservation groups were quick to claim there were too many deer. But he cited figures showing there had been a 10% drop in deer numbers in the Monadhliaths since 2004, by 26% in Knoydart in seven years and 14% in West Sutherland in seven years.
Dr Maggie Keegan, head of policy for the Scottish Wildlife Trust, said it was known that in some areas of Scotland, deer numbers were too high for the natural environment.
She added: " If we are going to reverse the decline to Scotland's most threatened habitats we may have to rethink the voluntary approach to deer management."