Police were blocked from boarding a US military aircraft at Prestwick Airport, despite concerns it may have been involved in terror rendition.
The CIA has been accused of using Scottish airports to facilitate the transfer of terrorism suspects to overseas blacksites for interrogation and torture.
A newly-published report from the UK Parliament's Intelligence and Security Committee (ISC) reveals MI5 or MI6 were involved in at least 50 rendition operations.
It is unclear whether any of those involved Scottish airports.
Police Scotland has been investigating rendition for several years, but in testimony to the ISC deputy chief constable Iain Livingstone acknowledged the force's hands have been tied.
In one instance, officers were prevented from boarding a plane at Prestwick carrying American senators.
He said: "Our colleagues in the Border Force were aware of an American aircraft at Prestwick having departed - I can't remember the specific country - North Africa.
"Border Force, acutely aware of potential allegations in the past around extraordinary rendition, wished to meet that aircraft and board.
"The chief immigration officers was seeking guidance in terms of what we can do. That involved having a conversation with the Americans, who provided them with some guidance.
"That guidance was that 'we can have the individuals on the aircraft come off and meet you on the tarmac, however you cannot come on board the aircraft'."
Scottish police had to watch "at a distance" while the Border Force met the Americans, "taking them at their word that there was no-one left on board their aircraft".
The Ministry of Defence told the ISC it was confident "no rendition flights are facilitated without our knowledge".
Human rights campaigners Reprieve claim Prestwick Airport functioned as a "crucial staging point", where rendition flights stopped to refuel.
Reprieve also alleges other Scottish airports have been "widely used by CIA jets".
Detective chief superintendent Gerry McLean, head of counter-terrorism at Police Scotland, said: "We continue to investigate this issue and provide regular updates to Crown Office.
"We were happy to give evidence to this House of Commons committee and our attendance there was facilitated through agreement with the Crown Office."
The ISC's report also reveals British intelligence agencies were aware of 153 cases where detainees were mistreated, as well as 13 where abuse was witnessed first-hand.
The ISC said there is no evidence British personnel directly physically mistreated detainees, however.