All airspace over London was shut on Friday afternoon because of a computer failure.
Traffic controllers at NATS said a technical problem occurred at Swanwick air traffic control centre.
Planes were being diverted away from the capital and flights at airports in the south of England were also suspended.
Heathrow said there were delays because of a power outage. Gatwick said there were no flights departing during the closure but flights were arriving.
Airspace was slowly opened up again from about 4.30pm when the issue was resolved at Swanwick.
NATs said: "Following a technical failure at Swanwick, the system has been restored.
"However, it will take time for operations across the UK to recover so passengers should contact their airline for the status of their flight.
"We apologise for any delays and the inconvenience this may have caused."
Both Belfast International Airport and Belfast City Airport warned that flights would be delayed, advising passengers to check with airlines for the latest information.