Planes were restricted from entering the affected area
Air traffic control systems are back up and running after an earlier computer breakdown at Prestwick grounded transatlantic flights from UK airports.
Some travellers may still experience delays due to the problem at Prestwick's air traffic control hub.
A spokeswoman for NATS, responsible for the UK's air traffic management, said engineers had resolved the problem.
Airports are now working to clear a backlog of flights which had been unable to leave due to the fault.
BBC transport correspondent Richard Scott said the computer had gone "zero rated" which meant it could not process any routings and everything had to be done manually.
The problem concerned Shanwick Oceanic Control, which is the airspace area for the north east Atlantic 250 miles west of Ireland.
BAA, the company which owns seven major UK airports including Heathrow and Gatwick, said they were working to get delayed passengers on their way.
"There are some delays still but it is getting back to normal," a spokeswoman said.
British Airways said not all of its flights were affected. Its statement said: "Air Traffic Control issues are affecting all airlines operating flights out of the UK on transatlantic routes.
"We, like all airlines, are experiencing some minor delays but our flights are still operating."
One passenger waiting on an American Airlines plane at Heathrow, Sam Mosley, said the airline had put them on the aircraft but said there could be a considerable delay.
"They said they would get us on the plane and see how it goes. Everyone's pretty stoic, we're just passengers waiting to get away," he said.