Crofters in the Gairloch Peninsula in Wester Ross claimed the birds of prey were responsible for the deaths of 200 lambs last year alone.
To find out whether sea eagles were slaughtering flocks, Scottish Natural Heritage funded a study that involved fitting 58 lambs with radio transmitters, which sent out a signal if the animal died.
Preliminary results show that none of the tracked lambs ended up dead in a sea eagle's nest.
RSPB Scotland has always maintained that the handful of white-tailed sea eagles in the area could not be responsible for such a large number of deaths, and a spokesman said yesterday he hoped the results of the study would "assuage" the concerns of the crofters.
The research, which cost almost 100,000, also involved an analysis of the nests of the four pairs of sea eagles in the area.
Some lamb carcases – not those being tracked – were discovered.
Forensic analysis of the blood patterns was used to determine whether these lambs were killed by the sea eagles or whether they were taken as carrion after they were already dead.
The number of lambs found in the eagles' nests is expected to be revealed when the full report of the study is published next month.
The analysis of the contents of the nests revealed the giant birds of prey were mainly eating seabirds.
Iain Ross, a spokesman for SNH, said: "The indications are that the level of lamb taking is nothing like what was suggested last year. "None of the lambs that were tagged ended up in a nest."
One person close to the study said: "If the sea eagles got through that many lambs, they couldn't fly for a start because they would be so full.
"There would need to be about 50 sea eagles. The skies would be black with them."
A spokesman for RSPB Scotland said: "There can be little doubt that the crofters do have some serious concerns about lamb losses.
"But attributing this to sea eagles in the way they did came as a great surprise to us because in our experience eagles do not take anything like that number."
However, Willie Fraser, chairman of the Gairloch and Poolewe branch of the Crofting Foundation, said he was convinced that the sea eagles were responsible.
He said: "I'm not surprised that the sea eagles did not take a single one of the radio-tagged lambs. The tags were so big and black it would have put the eagles off.
"They are still a major problem, though they have not been so bad this year. However, people started losing lambs again at the end of the study period after August."
He thinks a limit should be placed on the number of the birds in Scotland – and that plans to bring in even more from Norway over the next few years should be scrapped.
Sea eagles were persecuted to extinction in Scotland by the early 20th century.
However, they were reintroduced when birds were brought over from Norway in the 1970s. Numbers have reached record levels this year – with 46 breeding pairs and 36 chicks. Most live on Mull, Skye and the Western Isles. A more recent reintroduction programme has introduced chicks to Fife.