National Air Traffic Services (NATS) said a technical fault in the flight data system at its Swanwick centre in Hampshire had caused the problem Friday, BBC reported.
Earlier, the glitch caused several delays at the busy Heathrow and Gatwick airports, where flights waiting for departure remained grounded.
This resulted in a widespread disruption in airports around the UK Friday.
Transport Secretary Patrick McLoughlin said the situation was “unacceptable”.
The Swanwick centre was restored to “full operational capacity” by Friday afternoon, NATS said.
Heathrow Airport has cancelled around 16 flights Saturday and posted a message on its Twitter account, warning of possible “knock-on effects” from the earlier disruption and asked passengers to check their flight’s status.
Gatwick Airport said it will be operating a full service Saturday. Several other airports are also expected to operate their scheduled Saturday flights on time, according to their websites.