Lambs will be radio tagged and observed by field workers
The fortunes of 60 lambs are to be monitored from birth to weaning to help determine whether large numbers of livestock fall prey to sea eagles.
Crofters on Skye and in Wester Ross have claimed the UK's biggest raptors feed on their stock.
Lambs on two holdings in Gairloch, Wester Ross, will be radio tagged and observed by field workers.
Scottish Natural Heritage (SNH) has appointed FERA (Food and Environment Research Agency) to do the study.
SNH said the study aimed to provide a scientific measure of the true level of lamb deaths directly attributable to sea eagles as opposed to other causes.
The information will be gathered via radio transmitters attached to the lambs to track their movements and signal their demise rapidly after the time of death.
SEA EAGLE FACTFILE
The white-tailed sea eagle is the UK's largest bird of prey
It became extinct in the UK during the early 19th Century and the present population has been reintroduced
RSPB Scotland has counted 42 sea eagle territories in Scotland
Each death will be mapped and the carcass traced and recovered to allow a post-mortem examination to determine the exact cause of death.
SNH head of policy and advice, Ron Macdonald, said the investigation followed discussions with crofters, farmers and land managers.
He added: "The project will deliver an unprecedented level of detail for mapping the extent and cause of lamb mortality in typical Highland conditions which, in turn, will provide an assessment of sea eagle impact.
"The study will also provide recommendations on the management of stock and sea eagles so as to reduce potential conflict."
Last year, crofters said four holdings on the Gairloch Peninsula lost more than 200 lambs between May and September and were adamant that the majority were victims of the sea eagle.
Willie Fraser, a local crofter and member of the project steering group, said of the new study: "The most important outcome for crofters will be to help minimise this problem in the area and ensure the continued viability of sheep rearing as an economic activity in the west Highlands."
RSPB Scotland's Alison MacLennan, conservation officer for Skye, Lochalsh and Wester Ross, hoped the monitoring would address the worries and concerns of the crofting community.
She added: "It will build on the valuable recent study also funded by SNH on the island of Mull - the most densely populated area of Scotland for sea eagles - which showed that a fraction of one per cent of all lambs that died were due to sea eagle predation."
Funded by SNH, the study has been designed and agreed by a steering group consisting of crofters, the RSPB, Rural Payments and Inspections Directorate and the State Veterinary Service.
SNH is also funding a programme of enhanced sea eagle nest surveillance to identify the type of prey being carried by adult birds to feed their chicks.
Meanwhile, efforts will be made to reduce goose numbers on the Western Isles.
SNH aims to trial a scheme which will reduce the number of eggs that hatch. Geese numbers on Uist have increased by 60% since 1997 and SNH spokeswoman Shona Sloan said if successful, the project may have to run for some years to bring goose numbers down to manageable levels.