It is feared mineral hunters have been active on the Strathaird Peninsula, where a team recently discovered meteorite deposits from an impact 60 million years ago.
They contain mineral material from space that has not been found on Earth before.
Dr Simon Drake from Birkbeck, University of London, made the finds on Skye with colleague Dr Andy Beard.
He said: “About three weeks ago one of the students working on a project for us alerted us to the fact that our samples were being sold on eBay.
“This is a very small, fragile site and I’ve been working with Scottish Natural Heritage (SNH), trying to get some protection for the sites.
“This guy was selling the meteorite slices of rock for £9.99 per sample and he had at least 10 of them. We’re looking at about two football sizes having been taken out to provide these.
“This is going for the price of a fish supper, and it’s 60 million years old. It’s insanity, really.”
The seller was contacted and has now removed the items from the online auction site.
The owners of the meteorite site and a second area of interest intend to put up public notices, Dr Drake said, but he would like to see them designated Sites of Special Scientific Interest.
The team made the discovery while exploring volcanic rocks on the island which they thought were volcanic flow deposit.
When they analysed the rock they discovered it contained rare minerals - vanadium-rich and niobium-rich osbornite, which have never been reported on this planet.
The minerals have, however, been collected by Nasa’s Stardust Comet Sample Return Mission as space dust in the wake of the Wild 2 comet.
Scottish Natural Heritage said the unauthorised removal of any of the deposit could be in contravention of the Land Reform (Scotland) Act 2003.
Geologist Dr Colin MacFadyen said: “The recent discovery by geologists of meteorite deposits on Skye is yet another example of Scotland’s tremendous geological heritage and its distressing to find out that mineral hunters have been targeting the site.
“Reports that samples removed from Skye have been on sale via the internet is extremely concerning and disappointing as we understand that the meteorite deposit is vulnerable to damage and theft.
“We are working with the researchers and land owners to safeguard the deposits and ensure they are available for future research.
“We also appeal to people not to remove any of the deposit which has major scientific importance and help us keep an eye out for those who do.”