More than 100 flights have been cancelled and many others delayed after a major computer failure grounded planes in London and the South.
A glitch at the state-of-the-art UK air traffic control centre headquarters in Swanwick, Hampshire, caused severe disruption.
For a time no aircraft were able to take off at some of the UK's major airports. Some flights were allowed to land.
Transport Secretary Patrick McLoughlin said the disruption was "simply unacceptable" and revealed the Government had asked NATS for a full explanation.
It was reported airspace over London had been closed but air traffic control company NATS denied this, saying airspace capacity was "restricted in order to manage the situation".
NATS later said the system had been restored and it was in the process of returning services to normal.
The glitch lasted from 3.27pm to 4.03pm and Sky sources said a flight planning server had failed.
Airports affected by the disruption included Heathrow, Gatwick, Stansted and London City.
Aberdeen and Edinburgh were also hit by the computer problem. Other airports that reported delays included Birmingham, Manchester, Luton and Bristol.
Heathrow said at least 75 flights have been cancelled and up to 400 delayed.
It said the problem was likely to have a knock-on effect for flights on Saturday because aircraft and crew will not be in the correct positions.
Gatwick saw 15 cancellations and London City between 10 and 15.
British Airways said: "We are working hard to look after our customers who have been affected by the air traffic control failure experienced by all airlines at Heathrow, Gatwick and London City airports.
"We anticipate disruption to both departing and arriving aircraft but will do all we can to minimise any impact."
Speaking to Sky News, NATS managing director of operations Martin Rolfe defended his organisation's handling of the chaos.
"It was a technical failure at our Swanwick centre which handles 6,500 flights a day," he said.
"We went through our backup systems and restored things relatively quickly but not without delays to passengers, which we hugely regret.
"These things are relatively rare. We are a very busy island for air traffic control, so we're always going to be operating near capacity.
"What we've seen today is a very quick response. We didn't close any airports, we didn't close any airspace. We reduced the flow to make sure everything could be handled safely."
East Midlands and Birmingham airports said they were virtually unaffected.
One passenger caught up in the travel chaos was Matt Warren. He tweeted: "Stuck on the tarmac at Heathrow airport. Air traffic control failures. No flights in or out."
David Fitzgerald, who was stuck in a plane on the tarmac at Gatwick, should have been going to Dublin for a 3pm departure.
"We were boarding but then we were told the news there was a major failure at air-traffic control," he said.
"The good news is that some aircraft are being allowed to leave using a lower flight level - it's only the higher flight level that's affected."
Nick Adderley, a police chief superintendent, was also stuck on the tarmac at Gatwick after trying to fly home to Manchester.
He told Sky News: "This is a business flight for me… [I am] trying to get home after a business meeting in London.
"There are a number of people on board trying to get connecting flights to go on holiday. The spirits are pretty high. The mood is pretty good at the moment."
The centre at Swanwick has been subject to a number of computer glitches since NATS moved there from its old headquarters in West Drayton in west London in the early part of the last decade.
One of the worst problems was a year ago - on Saturday 7 December 2013 - when thousands of passengers were left stranded when hundreds of flights were grounded following a technical fault at the Hampshire centre.
