Experts say as many as one-third of the sites in the islands, such as the 5000-year-old Stone Age village of Skara Brae – one of the world's leading New Stone Age attractions – are at risk.
Tens of thousands of tourists visit them every year.
The University of the Highlands and Islands and Orkney's community archaeologist, Julie Gibson, said: "Scotland has the longest coastline in Europe and, as a maritime nation, much of our heritage relates to the sea. Around Orkney, more than one thousand archaeological sites are threatened or are being actively damaged.
"The 5000-year-old Stone Age village of Skara Brae is dependent upon a sea wall that requires constant maintenance, the medieval site of Langskaill in Westray retreated five metres in one go a few years back, and a Pictish site on Lamb Holm went from being a visible building to nothing but a line of rubble.
"Such erosion not only causes us to lose information about our past, but may also damage Scotland's future economy and the livelihoods of people in remote and rural areas.
"If these sites receive suitable investment, they have the potential to generate finds and media interest which will attract visitors from across the globe."
It came as Current Archaeology (CA), a leading archaeology magazine, focused on the rapid erosion which has revealed spectacular Neolithic and Bronze Age archaeology on the coast of the Orkney island of Westray.
It says the Links of Noltland on Westray boasts an impressive prehistoric landscape stretching over almost 10 acres including well-preserved remains of more than 20 buildings, "including Neolithic structures contemporary with, and comparable to, the famous "village" at Skara Brae.
It says it "is revolutionising knowledge of Neolithic and Bronze Age Orkney".
However, in the article, Carly Hilts, assistant editor, warns Noltland's archaeological features are in danger of being lost due to the severe risk of erosion, with the dune system that has protected it for millennia rapidly depleting.
She wrote: "By 2005 it was clear the scale of erosion was accelerating at an unprecedented level."
A spokesman for Historic Scotland said: "Archaeological research is vital to furthering our understanding of Scotland's rich and vibrant history in both coastal and inland communities.
"This research and eventual interpretation is recognised as an important contributor to the local and national economy by acting as a significant draw.
"In many locations coastal erosion is a major concern and something we are conscious of and actively work with local partners to mitigate its effects.
"On sites we manage, we routinely carry out assessments and conservation work to ensure these precious sites are protected from the elements and continue to act as a source of invaluable information about the history and heritage of our coastal communities."
l Ms Gibson will speak about the threat to Orkney's heritage as part of the Celtic Connections festival in Glasgow this week.