Sir Stephen refused to discuss how many people had travelled to the country as he warned some may have done so for genuine reasons.
It follows the release of a film of the killing of US journalist James Foley, with the film fronted by a masked man dubbed 'Jihadi John' last week. Abdul Raqib Amin, originally from Aberdeen, has also appeared in a film for the Ismalic State group.
Sir Stephen said: "There have been a number of high-level meetings at national level and in Scotland. We are working with the security services and the Met Police."