Wick, Aberdeen and Inverness airports were used in the rendition of terrorist suspects, a study has claimed.
The CIA programme involved the secret detention and transfer of terror suspects to other countries for interrogation and alleged torture.
Researchers at the universities of Kent and Kingston studied thousands of flights suspected of being involved.
They concluded that 13 planes with links to the CIA operation touched down at the airports.
Rob Gibson, the SNP MSP for Caithness, Sutherland and Ross, called on the UK government to "come clean" on what knowledge it had of the alleged CIA rendition flights.
The findings were made in work by Dr Ruth Blakeley at the University of Kent and Dr Sam Raphael at Kingston University in London.
The use of Prestwick, Glasgow and Edinburgh as a stop-off on journeys, often linking the US and Middle East, was already identified in their interactive online database.
The north and north-east links were not previously considered "suspicious" by the team but were highlighted for further investigation after details of flight paths emerged.
The study suggested five flights landed at Wick, a further five at Inverness and three at Aberdeen.
One aircraft which landed at Wick in 2004 has been "logged flying to secret prison and torture destinations", the researchers said.
It cannot be established if the planes had prisoners on board, only that aircraft were linked to rendition flights in the past.
The research looked at the system put in place following the September 2001 terror attack in the US.
The researchers' database has tracked more that 11,000 flights by more than 120 aircraft linked by past investigations to renditions.
A Scottish government spokesman said: "Responsibility lies with the UK Government, who state that permission for rendition flights would only ever be granted if the UK government was satisfied that the rendition would accord with UK laws and our international obligations.
"The Scottish government does not believe such flights could ever be in accordance with domestic or international law, and we would not expect such consent to ever be granted."