The Virgin Mary, at Haddo House, Methlick, was investigated at part of BBC Four's Britain's Lost Masterpieces.
It was acquired by George Hamilton-Gordon, the 4th Earl of Aberdeen and Prime Minister between 1852 and 1855.
Art experts Dr Bendor Grosvenor said: "Finding a possible Raphael is about as exciting as it gets."
Raphael - Raffaello Santi, who was born in 1483 - was considered the supreme painter of the High Renaissance era.
His work also extended to architecture and design.
The Virgin Mary was bought as a genuine Raphael, but it was later attributed to Innocenzo da Imola.
It was removed, cleaned and subjected to detailed investigation.
Dr Grosvenor said: "This is a beautiful picture that deserves to be seen by as many people as possible.
"I hope 'the Haddo Madonna', which would be Scotland's only publicly owned Raphael, brings many people to this part of Aberdeenshire."
Jennifer Melville, head of collections, archives and libraries at the National Trust for Scotland said: "The National Trust for Scotland holds so many treasures all over the country. We always knew that the collection at Haddo was very special, and the discovery of these wonderful pieces confirms its importance in the Scottish art world.
"It is rare for visitors to see works of this quality outwith a gallery, so it is a real treat to come to Haddo House and enjoy them in this wonderful setting.
"This is particularly exciting for the piece which looks likely to be by Raphael. There are not many places where you can experience the work of one of the Renaissance's giants in a dining room. It is this intimacy which makes exploring our collections quite so special."
Britain's Lost Masterpieces airs on Wednesday at 21:00.
A painting at a National Trust for Scotland property in Aberdeenshire is probably by famous Italian artist Raphael, experts have said.