Up to 10,000 passengers at Heathrow alone were affected by an air traffic control computer failure, the transport secretary has confirmed.
Patrick McLoughlin said Friday's failure was "unacceptable" but defended the National Air Traffic Services.
He told MPs he welcomed an inquiry by the Civil Aviation Authority (CAA) into the chaos, saying he hoped the findings would be available by March 2015.
Nats has blamed a computer glitch for disruption to flights across the UK.
Answering questions from the House of Commons Transport Committee, Mr McLoughlin defended the overall performance of Nats, saying it was doing "an incredibly good job".
"The average delay this year in Nats is 2.5 seconds per flight, whereas the rest of Europe we're taking about 30 seconds," he said.
He also compared the disruption to a telephone failure at the Swanwick centre in December 2013, which also caused flight disruption.
That incident caused 126,000 minutes of delays, compared to Friday's 16,000 minutes, Mr McLoughlin said.
Earlier, Prime Minister David Cameron said the failure - which has been blamed on a single line of computer code in one flight system - would be examined "very, very carefully".
The CAA is to appoint an independent chair to lead the inquiry, which will take evidence from experts on information technology and air traffic control.
However, the transport committee's chairman Louise Ellman questioned Mr McLoughlin about the inquiry - which could involve CAA and Nats staff - saying it "did not look very independent".
The inquiry would be dealing with a very specialised and technical area, Mr McLoughlin said. He said there was a limited number of people who could carry it out.
"We want to find out what went wrong and make sure it doesn't happen again," he added,
Investment by Nats has been questioned since Friday's failure, which grounded many flights at Heathrow and Gatwick with knock-on effects at other UK airports.
Heathrow also cancelled about 40 flights on Saturday morning before normal services resumed.
The company's chief executive, Richard Deakin, rejected criticism from Business Secretary Vince Cable, who accused the company of "skimping on large-scale investment" and being "penny wise and pound foolish".
The company says it will be spending £575m over the next five years on systems.
Mr Deakin has also faced calls from Labour MP Paul Flynn to have his bonus docked because of the disruption.
Speaking to BBC Radio 4's Today programme, he said he expected his pay to be affected by the incident but stressed that Nats' performance over the year had been good.
"We have the funding that we need to deliver the service that we require," he added.