The admission was made by the Nats chief operating officer, Colin Chisholm, who revealed in a talk to staff that cumulative delays for airlines and passengers reached 217,000 minutes in a seven-day period late last month.
Although the average delay per flight caused by Nats is less than three minutes, individual flights can be held up much longer. Last week Nats installed a software upgrade at Swanwick which was a factor in delays of an hour or more in England and Wales.
Eurocontrol, the European air traffic control centre at Brussels, has "strongly recommended" some airlines to find routes "avoiding UK airspace" on 25 July.
Chisholm's figures mean that in early July the delays due to air traffic control problems were equal to 3,600 lost hours in a single week. Chisholm described this as a "fairly dire" position for customers, who are mostly airline operators. Since his talk the delays have increased further, to 220,000 minutes last week.
Nats' predicament is a blow to the credibility of the purpose-built centre at Swanwick, which cost £623m, £337m of which was for a new air traffic control computer system from IBM and Lockheed Martin.
The centre became operational in January, nearly six years later than planned, in part because of problems developing two million lines of code.
Nats had told a House of Commons transport committee that when the centre opened, it would provide a 40% increase in capacity, and there would be extra staff available to ensure that the transition to Swanwick went smoothly.
But Nats has been hit by staff shortages and some controllers having difficulty reading computer screens.
Last year airlines expected delays because controllers' time was being split between normal duties and training to use the new Swanwick system - at times last summer delays reached record levels - but they had expected delays to be minimised once Swanwick went live. This year, however, weekly delay figures have increased by up to 100% in comparison with the same period in 2001.
Chisholm said the whole air traffic control team was working "desperately hard" to try to improve service.
A Nats spokesman said there had been enough controllers to open Swanwick and bring the centre up to full capacity by Easter 2002. Although Nats is short of 41 staff, "We have 62 controllers in training at Swanwick and the situation will improve as they validate [gain licences]," he said.
Delays have been exacerbated by a shift from long-haul to more low-cost flights, which impose higher demands on controllers, said the spokesman.
He added that last week's advice from Eurocontrol about avoiding UK air space was a "highly unusual" warning.