Delays and cancellations due to a technical problem at the National Air Traffic Service in Swanwick will continue into Sunday.
The problem has been fixed by NATS engineers, but the backlog will take time to clear.
Airports including Southampton, Gatwick, Stansted, Southend and Heathrow are affected, as are other UK airports including Edinburgh and Dublin.
Passengers are still advised to check with their airline for flight information.
In a statement, a spokesman for NATS, which controls the airspace in the UK with technical support from Lockheed Martin, also based in Swanwick, apologised to passengers and said the problem arose when a system to switch the system from night to day malfunctioned.
He said: ‘At night, when it’s quiet, sectors of airspace are combined. As it gets busier in the daytime the sectors are split out again and additional control positions are opened to meet the traffic demand.
‘Because of the problem with the internal telephone system, it was not possible to open the additional control positions this morning, resulting in a significant reduction in capacity in some areas of UK en-route airspace.
‘Safety has not been compromised at any time.’
In an update issued on Saturday evening, the spokesman added: ‘The problem that arose this morning with the ground communications system in the Area Control operations room at NATS Swanwick has now been resolved and operations are returning to normal.
‘The technical and operational contingency measures we have had in place all day have enabled us to deliver more than 80 per cent of our normal operation.
‘The reduction in capacity has had a disproportionate effect on southern England because it is extremely complex and busy airspace and we sincerely regret inconvenience to our airline customers and their passengers.
‘To be clear, this is a very complex and sophisticated system with more than a million lines of software. This is not simply internal telephones, it is the system that controllers use to speak to other ATC agencies both in the UK and Europe and is the biggest system of its kind in Europe.
‘This has been a major challenge for our engineering team and for the manufacturer, who has worked closely with us to ensure this complex problem was resolved as quickly as possible while maintaining a safe service.’