Around half of all flights in Europe could be delayed due to a fault with an air traffic management system.
The European Organisation for the Safety of Air Navigation, commonly known as Eurocontrol, warned that around 15,000 flights may be disrupted after it suffered a computer failure.
The issue affected a system that controls air traffic by analysing demand and capacity.
Flight plans submitted to Eurocontrol before 11.26am were lost and airlines were asked to resubmit the information.
A spokesman for the organisation, which has 41 member states including the UK, said: "We are very sorry about all the disruption and are working hard to get operations back to normal.
Luton-based airline easyJet said in a statement: "Due to an earlier flight failure of the Eurocontrol flight planning system, easyJet like other airlines experienced delays to some departing flights.
"Ten flights were delayed between one hour and three hours with 16 flights delayed as a knock-on effect caused by the initial delays. EasyJet will operate 1,598 flights today.
Budget airline Ryanair also confirmed some flights are experiencing delays and further delays are expected.
However Heathrow, the UK's busiest airport, said there was no impact on its operations.
Some 59% of departing flights at Gatwick were delayed between 3pm and 4pm, according to airline data company FlightStats.
A spokeswoman for the West Sussex airport was unable to immediately confirm that the disruption was caused by the system failure.
UK air traffic control provider NATS said the problem was unconnected to its planned airspace capacity restrictions which come into force on Wednesday as a new technology system is introduced.