Flight problems at some of the UK’s busiest airports stretched into the weekend after a system failure at the main national air traffic control centre in Swanwick on Friday afternoon.

There were 38 flights cancelled at Heathrow early on Saturday morning, “as a knock-on from yesterday”, according to a spokesman for the airport .

Planes were grounded and passengers experienced hours of delays and cancelled flights on Friday as London airspace was severely restricted for about an hour. Runways were closed for a period at Heathrow, Europe’s busiest airport, and Gatwick.

Flights which did land at London’s airports were unable to unload passengers with gates gridlocked. Others were taking off up to four hours late.

Flights started to depart again after 4.15pm, but passengers travelling to and from London’s largest airports faced lengthy delays and cancellations.

A Heathrow spokesman said on Friday there had been 70 cancellations out of about 1,300 scheduled flights.

Airports as far north as Aberdeen and Edinburgh were affected by the computer problem. Other airports that reported delays on Friday afternoon included Manchester, Stansted and Luton.

Budget flier easyJet said on Friday night: “EasyJet has had to cancel 10 flights to and from London Gatwick, however all aircraft which were earlier diverted have all now continued to their original destinations. In addition, it is likely that other flights to and from the south of the UK will suffer delays this evening.”

The airline said it had cancelled two Gatwick-bound flights scheduled for Saturday.

A message from Gatwick airport said on Friday evening: “Some cancellations should be expected and passengers are advised to contact their airline for the latest flight information.

“All departing flights were affected for a period but the situation is improving and we [are] hoping to restore a near normal service later this evening.”

In a statement on its website on Friday evening, British Airways said: “While the system is slowly recovering, we anticipate the knock-on effects to take some time to resolve. Additional staff have been brought in to assist our customers and we have booked a large number of hotel rooms to accommodate those who have been disrupted.”

Among the passengers waiting for information on outgoing flights at Heathrow on Friday was Claire Baron, a young South African, who needed to get to Zurich on Friday night in order to catch a long haul connection to Johannesburg.

“When you get to the front [of the queue] they’re saying that it takes 10 minutes to process and all they will do is give you a letter and a phone number,” she said, referring to long queues at Swiss Airlines. “‘They’re doing the best they can but I’m being fobbed off, [they’re] saying go home or get a hotel.”

Two Argentinian teenagers trying to get to Zurich for a connecting transatlantic flight had better luck. “We’re good at arguing. It’s in our culture,” said one, who added they had been rebooked on an early Saturday morning flight after lobbying officials and telling themthey did not want to queue for two hours. “I said that there was a special circumstance. My dog had to be put down today so I was in a really bad mood anyway.”

Air traffic controller Nats was able to restore its computer services after the unknown glitch but hundreds of international flights had already been diverted or disrupted.

Transport secretary Patrick McLoughlin said: “Disruption on this scale is simply unacceptable and I have asked Nats for a full explanation of this evening’s incident.”

A spokeswoman for Nats confirmed there was a technical failure at Swanwick, in Hampshire, the leading control centre for southern UK airspace.

She said: “The system has been restored. However, it will take time for operations across the UK to fully recover so passengers should contact their airline for the status of their flight.

“We apologise for any delays and the inconvenience this may have caused. We are investigating the cause of this fault but can confirm that, contrary to some reports, it was not due to a power outage.”

Experts said that a failure in some of the new upgraded software may have introduced a glitch. Doug Maclean, a consultant at DKM aviation, said: “The way the airspace is sectorised is designed to cope with this, so that if you have a glitch in one operations room, the whole of the UK is not affected.

“It sounds very much that it was the upper airspace sector which was affected, which means the contingency is that the London terminal area which handles the lower airspace would have taken over some of the flights.”

A computer problem affected operations at Swanwick for almost 12 hours last December, leaving thousands of passengers stranded as hundreds of flights were grounded.

Maclean said flights could normally still continue to a limited extent. “Because of the sheer volume of traffic, the first way that we deal with it is flow control. They simply stop all the traffic heading for airspace. If a plane’s on the ground it’s not a risk. But at its most basic, controllers can still talk to the planes because they’ve got radio systems.”

Prof Martyn Thomas, visiting professor of software engineering at Oxford University, said: “NATS has an outstanding safety record. They won’t have compromised safety, which always takes priority over delays, but delays were inevitable once the controllers lost the support of their computer-based tools, because without the tools the controllers cannot handle as many simultaneous aircraft.”

Aviation expert David Learmount told the BBC: “Because they don’t take any risks at air traffic control, they like to empty the skies. But because they have landed some planes, it shows they still have some capability.”