Ryanair has published details of flights cancelled up to the end of next month.
Customers affected will be emailed offers of alternatives or full refunds and details of their compensation entitlement, the budget airline confirmed.
It faces a compensation bill of up to 20 million euro (£17.7 million) for the "mess" which has left many passengers stranded, boss Michael O'Leary said.
The Dublin-based carrier is shelving up to 50 flights daily over the next six weeks due to the over-allocation of pilots' holidays during a relatively busy period.
They have been listed on www.ryanair.com and cover the period up to October 28.
The airline said it was cancelling flights at airports where it ran the busiest schedules, so it would be easier to place passengers on alternative flights.
Mr O'Leary, the airline's chief executive, told a press conference: " Clearly there's a large reputational impact, for which again I apologise. We will try to do better in future.
"In terms of lost profitability, we think it will cost us something of the order of up to about five million euro (£4.4 million) over the next six weeks and in terms of the EU261 compensation we think that will be something up to a maximum of 20 million euro, but much depends on how many of the alternative flights our customers take up."
Mr O'Leary said customers whose flights have been cancelled will receive an email by Monday evening.
This will inform them what flights they can transfer to which will be "hopefully on the same or, at worse, the next day".
Under EU law, passengers given less than 14 days notice of a flight cancellation are entitled to claim compensation worth up to 250 euro (£221) depending on the timing of alternative flights and if the issue was not beyond the responsibility of the airline, such as extreme weather.
Mr O'Leary said: " If they're not satisfied with the alternative flights offered, they can have a full refund and they will all be entitled to their EU261 compensation entitlements.
"We will not be trying to claim exceptional circumstances.
"This is our mess-up. When we make a mess in Ryanair, we come out with our hands up.
"We try to explain why we've made the mess and we will pay compensation to those passengers who are entitled to compensation, which will be those flights that are cancelled over the next two weeks."
Mr O'Leary insisted the airline is " not short of pilots" as he explained the reason behind the cancellations.
He said: " What we have messed up is the allocation of holidays and trying to over-allocate holiday during September and October while we're still running most of the summer schedule, and taking flight delays because of principally air traffic control and weather disruptions."
Changes imposed by Irish regulators, in line with European law, forced Ryanair to conform staff holidays with the calendar year from January, requiring it to allocate that leave before the end of the year.
Asked if he believed he should lose his job, Mr O'Leary replied: "No, I don't think my head should roll, I need to stay here and fix this."
The routes affected include flights to and from Dublin, London Stansted, Barcelona, Lisbon, Madrid, Milan Bergamo, Porto and Rome Fiumicino.
Alex Neill, a managing director at Which? consumer service, said: "It's vital that passengers who have suffered the nightmare of Ryanair's cancelled flights are now given clear information about what they are entitled to.
"Ryanair must quickly honour its legal duty to arrange alternative flights or provide a full refund, as well as reimbursing reasonable out-of-pocket expenses.
"The airline will know which passengers are entitled to compensation and should pay this out automatically, so they don't have to go through the additional stress of trying to claim what they are rightly owed."