The National Air Traffic Service said its computer system went down at about 6 a.m. The system was running again two hours later, but airports said the backlog of flights would cause delays throughout the day.
"Our computer system is now fully operational and safety being our primary concern, we are now working to make sure those aircraft in the air and in need of landing should be able to do so to clear the delays," air traffic spokesman Adrian Yalland said.
He said the problem may have originated at an operations center in West Drayton, near Heathrow Airport, which controls air traffic over southeast England and all planes into and out of London's airports.
The air traffic service has been beset by problems since it was partially privatized in 2001. A $484 million center at Swanwick in southern England opened five years late in 2002.
The opening was delayed by problems with computer software, and the glitches continued for months afterward, as controllers misread aircraft altitudes and destinations because of hard-to-decipher computer screens. In at least one case, controllers mistook the Scottish city of Glasgow for Cardiff in Wales.
The company also was hit financially by the fall in trans-Atlantic traffic following the Sept. 11, 2001 terrorist attacks.
Transport Secretary Alistair Darling said Thursday's problem did not lie at Swanwick but at the older West Drayton center, which is due to be closed by 2007.
"If you want to know what is wrong with transport in this country it is that over decades successive governments did not spend enough on the infrastructure and air traffic control is no different," Darling told BBC radio.
However, he added, "The air traffic control system in this country is very good compared with other countries. We are putting the money in, it is making a difference."