The RAF has suspended Typhoon training flights after deposits of volcanic ash were found in the engines.
But the Civil Aviation Authority (CAA) tonight said the RAF's "precautionary measure" will not ground passenger flights.
The incident led to checks of all Eurofighter jets based at RAF Coningsby in Lincolnshire.
The grounding of the £69 million fighter jets comes just two days after UK skies were reopened following an Icelandic volcanic ash cloud which stopped all flights over the UK for almost a week.
But the CAA stressed that military plane engines were very different to those of civilian aircraft and the Typhoon incident would not have an impact on passenger plane movements.
Revised airspace guidance for civilian aircraft was drawn up earlier this week by the CAA in a move which enabled UK airspace to reopen.
The guidance requires airlines to make damage inspections before and after flights and to report any ash-related incidents to the CAA.
The CAA said that so far there had been "only a very few reports from airlines and, of these, all related to visual sightings".
The CAA spokeswoman added: "There have been no reports of damage to aircraft."
The MoD said training flights were suspended until technicians could ensure the ash had not caused any engine damage.
A spokesman added: "These are very high-performance jets so they are just being extra cautious.
"They were flying as normal yesterday. Operational flying will continue."
Meanwhile, with airlines running near-normal services again, thousands of Britons were able to head back to the UK today.
Around 2,200 of the stranded tourists were sailing back from Bilbao on a new £500 million luxury cruise ship sent out on a rescue mission.
As travellers returned, budget airline Ryanair performed a U-turn on reimbursing passengers.
Yesterday, the Irish no-frills carrier's chief executive Michael O'Leary said he would reimburse travellers only the original price of their air fare and no more.
But today the airline said it would comply with the regulations under which EU airlines are required to reimburse the "reasonable receipted expenses of disrupted passengers".
Both Mr O'Leary and Ryanair stressed that this was not compensation, merely reimbursement. Mr O'Leary said that if claims were not reasonable, they would not be met.
Transport Secretary Lord Adonis welcomed what he described as Ryanair's "revised statement", saying the Government and the CAA had told Ryanair "in the strongest terms" that they were expected to comply with the EU regulations.
Liberal Democrat transport spokesman Norman Baker had been critical of Mr O'Leary's initial defiance of the regulations.
Later, shadow transport secretary Theresa Villiers said a Conservative government "would conduct a wholesale review of the rules governing compensation and travel insurance arrangements for air passengers".
Mr O'Leary said the EU regulations were "absurd and discriminatory" and that he would continue to work with other bodies to get the regulations changed.
He also said European governments and regulators had been wrong to apply a blanket ban on flights.
Some passengers arriving on Ryanair flights at Stansted Airport in Essex today were sympathetic to airlines' plight over reimbursement.
Victor Antwi, 37, from Sheffield, who flew in with a family party of 14 after a holiday in Portugal, said the group should have returned to East Midlands Airport on April 15 and estimated that he and relatives were several thousand pounds out of pocket.
"Ryanair is going to pay, hopefully," he said. "I do sympathise with what the airlines are saying - that the law was not designed for this kind of 'act of God'. I can understand that argument. But really, I don't care who pays as long as someone does."
Budget airline easyJet, which ran a full service today, said it had already paid for 100,000 hotel nights for stranded passengers.
The low-fare carrier added that it was likely to be able to get those stuck abroad home more quickly than first thought, as there was more room on flights due to passengers with reservations making other arrangements.
Three main London railway stations - Victoria, Paddington and Liverpool Street - will remain open all night again tonight and for the next 48 hours, as will Gatwick Airport station in West Sussex.
Railway lines serving Heathrow, Gatwick and Stansted Airports will also operate through the night and extra services will run into the early hours to serve the main ferry ports, including Dover.
Engineering work on the main London to Scotland routes - the East and West Coast Main Lines - has been cancelled to enable more direct services to run.Reuse content