The latest discovery, made late yesterday afternoon, is a stone with a zigzag chevron pattern in red pigment.
It is thought the painted and decorated stones may have been used to enhance important buildings and may have been found in entranceways or areas of the building which had particular significance.
Nick Card, of the Orkney Research Centre for Archaeology (Orca), said: “I think the Neolithic people were no different from ourselves in that these were probably special structures which they felt should be adorned in different colours.
“There has been evidence at some other Neolithic sites where paint pots have been found with remains of pigment but they were considered to be for personal adornment rather than being used on a wider scale for the decoration of buildings.
“This is a first for the UK, if not for northern Europe.
“The use of colour in this particular way was always suspected but this is the first concrete evidence we have of it.”