The waves have undermined a section of the concrete toe on which the protective walling was built and could cause damage if left unrepaired.
Historic Scotland has started a project which will involve digging two metres down, to insert a new reinforced concrete toe with steel securing rods to bond the existing toe to the underlying bed rock.
Stephen Watt, Historic Scotland district architect, said: "This is an important piece of work along a 15-metre stretch of wall and will involve a considerable amount of highly skilled work.
"The area affected is a bit beyond Skara Brae itself, but it is important because it stops the sea outflanking us. These are interim measures which help protect an enormously important part of Scotland's heritage.
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"We are currently working with a number of other groups and organisations to put together a strategy to protect the entire bay from the effects of natural erosion."
This year Historic Scotland will also be trying out two alternative surfacing materials on paths at Skara Brae.
Both have been a success at Stonehenge and may prove a hard-wearing and visually sympathetic alternative to the existing hard stone paths used in Orkney.
Mr Watt said: "A group of us travelled to Stonehenge last summer to see what we could learn from their experience in developing path surfaces that are long-lasting, easy for visitors to use, and do not look out of place near an ancient monument.
"We were very impressed with what we found. In some places they have a special turf which can take a lot of wear and tear and elsewhere they have artificial green matting which is coloured to blend in with the surroundings and is very slip resistant."
"We are going to try these out in a couple of areas and monitor them for 18 months to see if they would be appropriate at Skara Brae," he said.
A stretch of artificial matting will be laid in coming weeks and turf will be introduced in the spring - neither project will interfere the Skara Brae visitor experience.
(GK/JM)
