The continent-wide system which determines when and where planes can safely fly, land and take-off failed at about lunchtime on Tuesday, the European Organisation for the Safety of Air Navigation (Eurocontrol) said.
Half of flights across Europe face being delayed by the failure of the Enhanced Tactical Flow Management System (ETFMS).
About 10% of flights will have to be cancelled, the Brussels-based organisation said.
Airlines have been asked to refile any flight plans for flights which have yet to take-off.
Brussels Airport said it is only allowing 10 flights an hour to depart due to the failure.
Amsterdam’s Schipol Airport said some flights may be delayed, with passengers asked to check online before leaving for the airport.
A spokeswoman for London Heathrow said the airport is not expecting to have any delays due to the failure and it is “business as normal”.
Eurocontrol covers 41 states across Europe and has agreements with countries in northern Africa, the Middle East and central Asia to ensure air traffic flows safely and as smoothly as possible.
The failure comes a day before air-traffic control procedures in south-east England are overhauled as they switch from a 20th Century system using paper strips to an electronic tool.
Heathrow and Gatwick Airports have been given permission to allow 10 extra flights each to fly in after 11.30pm and before 6am for 10 days to ensure there are no spikes in air traffic so controllers can adjust to the new system.