Airports were almost back to normal yesterday, but airline and travel industry anger continued at the way the security crisis has been handled.
Ryanair, which had to cancel eight flights at Stansted, accused airport operator BAA of "a chronic inability to staff security facilities".
And British Airways said BAA's advice about yesterday's flights had come too late to prevent it having to axe 41 flights at Heathrow.
BA also said that due to the disruption of the last few days, it was still trying to reunite 5,000 pieces of luggage with their owners.
And the Federation of Tour Operators said travel companies had felt "let down by inconsistent airport policies and clearly inadequate staffing arrangements".
FTO chairman Ian Ailles said charter airlines had avoided cancelling flights and that delays had not been too bad.
But he added: "We feel let down, however, by inconsistent airport policies, clearly inadequate staffing arrangements and lack of rehearsed contingency planning which have made this serious situation far worse for customers than it needed to be.
"It is not clear to us how airport security arrangements at times of heightened tension have improved in the five years since the September 11 tragedy.
"We call for an independent inquiry, in the weeks to come, of the handling of this crisis by all the parties involved - especially the airports and the Government's own planning for passenger security in the light of this long-recognised potential threat."
Ryanair chief executive Michael O'Leary said his airline had seen a ten per cent drop in group bookings over the last couple of days as a result of the travel disruption.
"We're seriously considering taking legal action against the Government to force them to get the airports back to normal," he added.
British Airways announced last night it was cancelling 46 of its flights out of UK airports today - five more than yesterday.
In a statement, BAA said it "acutely regretted" the disruption the new security arrangements had caused to passengers and airlines.
The company said: "From the point at which the heightened security measures were imposed, we have been aware in great detail of the frustrations experienced by airlines operating from our airports.
"We continue to do everything we can to respond to the airlines' needs, but we will not compromise on our responsibility to apply the security regime the Government judges necessary to protect the public."
It hit back at criticism over its ability to deal with the situation, especially at Heathrow.
The statement continued: "Heathrow, in particular, has been singled out for criticism and the allegation has been made that BAA lacked adequate plans to deal with the emergency. We regret these comments, which are neither fair nor accurate.