Concerned farmers are now calling for radical changes in land management to encourage the return of natural prey, such as hares, for the giant birds to feed on.
Iain Maciver, chairman of the Lewis and Harris Sheep Producers Association and a former chairman of the old Scottish Crofters Union, said nine ewe hoggs - the stage between lambs and sheep - had been found dead on the Lochs area of south Lewis.
He said white-tailed or sea eagles were witnessed at the scene.
The RSPB is sceptical about whether eagles are to blame but Mr Maciver wants organisations such as the bird charity, which enthusiastically supports the reintroduction of the giant raptor across the Highlands and Islands, to direct resources to help crofters encourage wildlife as prey.
He said the nine hoggs had been reared for breeding purposes, so their loss was significant to the young crofter affected.
Mr Maciver said: "The crofter saw two eagles rise from down the hill. When he got there he found a dead hogg and eventually another seven dead."
He then realised another hogg was missing and saw a sea eagle take off, Mr Maciver said. "So he went in that direction and found a ewe hogg that had previously been counted alive, was now dead. It was still warm, but its throat had been cut and its rib cage punctured," he added.
He said historically there have "always" been golden eagles on Lewis. "Man and eagle have lived well with one another," he said.
But Mr Maciver said areas such as moorland which had previously been stocked were now largely used only by walkers and bird watchers and this had its impact upon wildlife in the area.
"A marked reduction in moorland and grazed areas has meant the wildlife has been affected as well," he said. This meant the sea eagles found it harder to find food such as hares.
He said crofters found existing eagle management schemes too bureaucratic and the compensation insufficient.
"The likes of RSPB Scotland and the John Muir Trust (JMT) seem happy, in my view, to boast about the depth of their resource and influence when they are minded to block development," he said.
"Directing some of these strengths towards the promotion of land-management incentives to encourage crofters to better exploit the grazing potential of our moorland could be a key factor in allowing man and bird to live in harmony, at the same time enhancing the quality of our wonderful environment."
An RSPB Scotland spokesman said there was little evidence to suggest sea eagles would predate fully grown sheep, although the incident would be thoroughly investigated by Scottish Natural Heritage (SNH).
He said RSPB accepted some occasional lamb predation by sea eagles would occur and acknowledged this situation "causes issues for some farmers and crofters".
SNH's sea eagle management scheme made annual payments to relevant farmers and crofters, and had been designed with their representatives to address these concerns.
Ross Lilley, SNH's Argyll and Outer Hebrides operations manager, said it would consider measures such as providing food for sea eagles if it did emerge sea eagles were responsible for the deaths.
He added: "Mr Maciver's comments are timely, as we're reviewing our national sea eagle management scheme at the moment, and these are exactly the kind of on-the-ground suggestions we are looking for.
"We have provided food for sea eagles occasionally in the past and it could be one of the measures we support in the future as part of a package of measures tailored to individual circumstances.
"If anyone else has suggestions, I would encourage them to contact us. Mr Maciver also makes a good point about improving moorland habitat, and this is something we are working on through programmes like the Scottish Rural Development Programme."
The wildland charity the JMT did not want to comment.