The details of the glitch were unclear; but the National Air Traffic Control Service told the BBC it would be later in the day before it was corrected.
Flights at London's Heathrow and other major airports experienced delays, and NATS cautioned travelers the ripple effect on schedules would likely continue once the system is back on track.
The BBC said the problem was with an internal NATS communication system, and it has left controllers unable to pass information among one another, so they can't manage as many flights as usual.
For passengers, delays ran around 40 minutes at Heathrow. NATS warned some passengers could be stuck for hours.