A passenger who said he had been waiting five hours at London's Gatwick airport earlier told the BBC that people had been "crying, distraught and angry".
Leeds Bradford, Doncaster Robin Hood and Newcastle airports all le prono unique reported minor delays, with flights to London worst affected.
In a statement it acknowledges that problems occur, but asks the question "where is the contingency?".
Live updates For live travel updates follow BBC Travel News UK which covers delays across the country BBC Travel News Air At Stansted, Alena Kontza was stuck on a Ryanair plane that had been delayed for three hours.Nats said the problem at its Swanwick centre, in Hampshire, arose in the early hours of offre reduction fragonard Saturday morning when the night-time operation failed to properly switch over to the daytime system.Media playback is unsupported on your device Media captionNational Air Traffic Systems: "We are not able to meet the demands" A spokeswoman for British Airways said: "We are organising hotels for customers when appropriate."One passenger has missed their sister's wedding Tom Flatman, from Brighton, said.It pointed out that customers could claim assistance from their airline if they were delayed for several hours, including being given food and drink, usually in vouchers.By Saturday evening Gatwick airport said it was "returning to normal operations".
Delays at Stansted averaged two to four hours, a spokeswoman for the airport said, adding that schedules were expected to return to normal on Sunday but warning there could be "minor delays".
"This is not simply internal telephones, it is the system that controllers use to speak to other air traffic control agencies both in the UK and Europe and is the biggest system of its kind in Europe.".Meanwhile, elsewhere: A spokesman said Manchester Airport had been "only minimally affected" and operations were now back now back to normal.Even so airline Ryanair isn't happy at having to cancel and disrupt so many flights.A spokeswoman for Birmingham Airport said around 60 flights were affected, the majority were delayed by under an hour.Claims can be made for flights that were delayed up to six years ago.In addition, customers on cancelled services of course have the opportunity to claim a refund or rebook." Independent aviation analyst Chris Yates said it had been a "trying and a very tough day adding: "There's going to be a lot of hard questions asked.Image caption At Heathrow's Terminal 3 the queues stretched outside the building.Thousands of passengers faced cancellations and long waits after the National Air Traffic Service (Nats) internal phone system broke down.No Easyjet flights have yet been cancelled but many were subject to delays.Media playback is unsupported on your device.'Severely delayed by 16:00 GMT Nats said it had handled 2,576 flights compared with 2,905 at the same time last week.Analysis, by Richard WestcottBBC transport correspondent, a fault with a complicated internal telephone system brought delays and cancellations for thousands of travellers today.Airlines should always provide refreshments after a two-hour delay and accommodation if it the flight is delayed overnight.Nats announced at 1930 GMT that the problem had been fixed, but some airports said delays could continue into Sunday.Belfast International Airport and Dublin Airport reported a number of cancellations.