Flights were delayed and airline passengers were left stranded after a computer systems failure at the West Drayton air traffic control centre last Friday.
Problems occurred in the UK Flight Data Processing System, which runs on IBM 4381 mainframes.
This prevented the print out of flight strips, paper flight plans used by air traffic controllers.
National Air Traffic Services (Nats) told Computer Weekly, "Safety was not affected. There was no interruption to radar information on controllers' screens or to radio communications.
"Flight strips are prepared well in advance and there were no problems with aircraft in UK airspace or on their way to the UK."
With controllers resorting to manual techniques, traffic volumes were cut by up to 50%. This meant hundreds of aircraft were delayed and British Airways cancelled 12 flights.
Nats said the failure was caused by a "specific combination of manual data inputs, which had not previously occurred before", in the system that handles several million flight plans a year.
The system was restarted and changed to prevent a repeat of the problems. However, Nats conceded that technical experts are investigating the glitch.
"Revised software will be produced, tested and introduced at the earliest opportunity," a spokesperson added.
The flight strips system will be used at the much-delayed Swanwick control centre, and the failure comes at an embarrassing time for Nats as the Government prepares it for partial privatisation.