Britain’s air traffic control chief was clinging to his job last night after the Prime Minister refused to back him over a second technical meltdown in two weeks.

Thousands of passengers were left stranded after hundreds of flights were grounded due to a ‘connectivity issue’ at the National Air Traffic Services (NATS) offices in Prestwick, Scotland.

Chief executive Martin Rolfe, who was already facing calls to quit after a computer error saw 2,000 flights cancelled 13 days ago, was under intense pressure yesterday as airlines said they had had enough.

Unlike the last glitch at NATS, which is 49 per cent owned by the taxpayer, Andy Burnham did not ride to Mr Rolfe’s defence yesterday.

Asked why he has not been sacked, the PM told reporters: ‘Well these are clearly serious issues and they need to be fully investigated, and I know the Transport Secretary is taking these issues extremely seriously.

‘Further issues today do cause even greater concern, but initially this is a matter for the Transport Secretary to get to the bottom of what is behind this and why there has been a recurrence.’ Earlier the PM’s spokesman had called the situation ‘deeply frustrating’ and said national infrastructure must be ‘fit for purpose’.

Transport Secretary Heidi Alexander said: ‘I know this will be deeply frustrating for passengers after the previous issue.’

Ryanair boss Neal McMahon said more than 25,000 passengers were affected and 140 of its flights delayed. ‘Martin Rolfe has presided over repeated system failures, repeated passenger disruption and repeated failures to deliver an effective back-up system,’ he said.

National Air Traffic Services chief executive Martin Rolfe, pictured, was under intense pressure yesterday as airlines said they had had enough

‘Enough is enough. Martin Rolfe should resign today.’

Beleaguered Mr Rolfe, 54, has presided over four major failures in recent years. He is the highest-paid air traffic controller in Europe, earning £1.4million last year and more than £6million over the past five years. By comparison, his Dutch counterpart, Joost Meijs, is paid £225,000 a year.

According to the UK Civil Aviation Authority, passengers are unlikely to receive compensation for yesterday’s delays and cancellations because they were due to an ‘extraordinary circumstance’.

Aviation analytics firm Cirium said EasyJet was the worst-affected airline followed by British Airways, Loganair, Ryanair, Aer Lingus and KLM. Flights were cancelled and delayed at London City, Heathrow, Luton, Manchester, Liverpool, Bristol, Glasgow, Edinburgh and Belfast airports.

Tim Alderslade, chief executive of industry body Airlines UK, said the air traffic control system was ‘critical national infrastructure’ which ‘must be resilient enough to keep people moving’.

‘Yet another NATS failure is causing delays and disruption for passengers and airlines alike, and comes just days after its report into the most recent major outage,’ he said. ‘Passengers and airlines deserve better.’

He added that inquiries into other recent failures ‘must address the underlying weaknesses in the system’.

Among those affected yesterday were Barbara Ann Stoddart and Andrew Lithgow, who were due to be flying to Las Vegas for their wedding. Their flight from Glasgow to Heathrow was cancelled, meaning they missed their transatlantic connection.

‘I’m completely stressed out,’ Ms Stoddart said.

NATS said the situation was being treated ‘very seriously’.

‘In the real world we accept technology can and sometimes does fail,’ a spokesman added.

‘Our job is minimising disruption where possible.’