Sites in jeopardy include the Neolithic settlement of Skara Brae on Orkney and the prehistoric ruins at Jarlshof on Shetland. Others under threat range from Viking burial boats to Iron Age brochs and Mesolithic middens, the study by the Scottish Coastal Archaeology and the Problem of Erosion (Scape) has said.
Archaeologist Tom Dawson from the University of St Andrews said, that remains of communities up to 9000 years old could be lost forever due to accelerating coastal erosion.
"The potential loss is incalculable. This is a uniquely valuable and totally irreplaceable part of the nation's cultural heritage, with much still to teach us about our past," said Dawson.
"While people argue over whether climate change is leading to sea level rise and an increase in stormy weather, the coast continues to erode. Although wildlife and the natural habitat may be able to recover, ancient sites will be destroyed forever, and the remnants of our ancestors will be lost," he said.
So far, Scape has surveyed 30 percent of Scotland's coastline, discovering 11,500 archaeological sites of which some 3500 have been judged to be at risk of erosion.
Dawson said many of the archaeological sites are concentrated on Orkney, Shetland, the Western Isles and parts of the west coast, which are known to be particularly vulnerable to storms. Others can be found around all the major estuaries, including the Clyde and the Forth, he said.
He said many sites have yet to be excavated and properly studied.
"Others are iconic and well-known remains defended by old and eroding seawalls, such as Skara Brae, Jarlshof, the Broch of Gurness on Orkney and Lochranza Castle on the Isle of Arran," the Sunday Herald quoted Dawson as saying.
Dawson said, while it would be impossible to save all the sites, it was nevertheless important to try to map, study and preserve as many as possible in order of priority. "It is not all doom and gloom. By working together, we can rescue information and artefacts from some of the sites before they are destroyed," he said.
According to the paper, a Shorewatch group is presently drawing and photographing the remains of a Pictish building, which is being eroded at Sandwick on Unst in Shetland.
There are also plans for another "adopt-a-monument" team to excavate an ancient Bronze Age structure at risk from the sea on the island of Bressay in Shetland.
Dawson said archaeologists and volunteers are also working extensively to record a mass of archaeological remains at Baile Sear, including pottery, animal bones, slabs of masonry and an ancient waste dump, uncovered earlier this year in a storm.