Several flights from Scottish airports to England have been delayed by up to 1 hour and 50 minutes, the Edinburgh Evening News reports.
A spokesman confirmed to the Independent that some flights to and from Northern Ireland have also been affected.
A statement from NATS said there had been overnight interference with the radio frequencies used to speak to aeroplanes.
It said: "It only affects part of Scottish airspace and flights from some Scottish airports this morning may be delayed as a result.
"We have identified the cause, isolated the problem and the situation is improving.
"We apologise sincerely for any inconvenience."
The NATS base in Prestwick controls all air travel between 2,500ft and 66,000ft over Scotland, Northern Ireland, northern England, the Midlands and north Wales, as well as the airspace over the eastern half of the North Atlantic.
Passengers at airports in Scotland tweeted their frustration with several saying they were stuck on the runway.
Marvellous, a major malfunction of the air traffic control system in Scotland. Now sat in a plane in Glasgow Airport and can't take off
โ Stephen Malcher (@malches67) October 26, 2015
Scottish air traffic control problems, looks like a computer glitch. Stuck on runway at Edinburgh no sign of moving - nothing on news
โ Eileen Thomson (@sunshineonleith) October 26, 2015
Edinburgh, Glasgow and Aberdeen airports confirmed they were experiencing delays on Twitter but said they were working to restore order as soon as possible.
A spokeswoman for Belfast International Airport could not be reached for comment.
Passengers have been advised to contact their airline to confirm whether their flight has been delayed or cancelled
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