Ryanair boss Michael O'Leary has admitted the cancellation of flights due to pilot holidays is "a mess".
The budget airline is under pressure to publish a full list of the flights it plans to cancel over the next six weeks as customers have become increasingly angry.
It said it was shelving up to 50 flights daily after an error in the planning of pilot holidays.
Chief executive Michael O'Leary told Sky News: "It is clearly a mess."
Some customers said last-minute cancellations have left them out of pocket due to non-refundable accommodation costs, or with no choice but to book expensive alternative flights or transport.
Others said they had been left stranded in their holiday destination.
UK aviation minister Lord Callanan said he is "very concerned" by the Dublin-based carrier's cancellations.
Under European Union laws for cancelled short-haul flights, airlines must offer a refund or book passengers onto another of their flights to the same destination.
If an alternative airline is flying there significantly sooner then passengers may have the right to be booked onto that flight instead.
Passengers who receive less than 14 days' notice of a cancellation which was not the airline's fault, such as due to severe weather or air traffic control strikes, can also claim compensation up to 250 euro (£220).
A European Commission spokesman told a press conference on Monday that "airlines operating in the EU need to respect the European rules".
He went on: "We have to check if all this is respected by Ryanair.
"For instance, you are entitled to reimbursement if you are not warned two weeks in advance."
Over the weekend the airline published a list of affected flights up to Wednesday.
Rory Boland, travel editor of consumer group Which?, said it is "essential" that Ryanair releases a full list of flights that will be affected to give passengers "as much time as possible to make alternate arrangements".
It was reported that recruitment problems were affecting the airline and it had lost a significant number of pilots to low cost rival Norwegian Air, something denied by Ryanair.
Mr O'Leary said: "We're working very hard at the moment to make sure we finalise the list of flight cancellations, which will affect less than 2% of our customers, and also look after those customers who are disrupted."
Changes imposed by Irish regulators, in line with European law, forces Ryanair to conform staff holidays with the calendar year from January, requiring it to allocate that leave before the end of the year.
Ryanair said air traffic control delays and strikes, bad weather and a backlog of annual leave to be taken by pilots and cabin crew had led to punctuality falling to below 80% over the last two weeks.
A spokesman said this figure was "unacceptable" and the company has apologised to affected customers, who it said will be offered alternative flights or refunds.
The vast majority of UK cancellations affected Stansted. Some Dublin flights were also dropped.