Although the galleries have not established that any of the works were stolen, they are contacting dealers to discover more about the history of 133 items acquired since 1933.
The works under scrutiny include items from Scotland's National Gallery, its National Portrait Gallery and National Gallery of Modern Art.
"Nearly 50,000 works have been examined," said a spokeswoman for the galleries. "The number we are concerned about is a preliminary figure. The problems with them may merely reflect the fact that a file has been lost or that an owner died suddenly, breaking the provenance. It is far too early to say whether any ... were taken from their rightful owners by the Nazis."
She added that since about 20 of the works are in the National Portrait Gallery, most of whose works are of Scots, it was unlikely that they would turn out to have a Nazi past.
Responding to criticisms from the Holocaust Education Trust, the spokeswoman denied there had been any delay in publishing the list of works, and insisted the galleries were working as fast as possible."The National Galleries of Scotland fully recognise the sensitivity and urgency of the issue of Nazi-looted art which is precisely why this research is being undertaken ... It would cause unnecessary pain and anxiety if the wrong information were released prematurely."
Earlier this year, the National Gallery in London concluded that 120 of its 2,400 paintings were of doubtful provenance. Of these, there are strong suspicions about 10, including two Monets.
Sir Nicholas Serota, who chairs the working party on Nazi-looted art, will convene a meeting later this month of more than 20 museums and galleries to assess how many doubtful works of art are held in Britain. Yesterday, he said: "No other group of museums in the world has addressed this issue so seriously or set out to research their collections so thoroughly."