Ryanair has said the cancellation of between 1,500 to 2,000 flights over the next six weeks happened because it "messed up the planning of pilots' holidays".
The airline says it regrets this and is working hard to fix the problem, and to make sure it doesn't happen again.
In a statement, Chief Marketing Director Kenny Jacobs said the airline apologises to "the small number of passengers affected" and said they can take a full refund or travel on a later flight.
Ryanair has not published a list of the flights affected and said it will contact passengers directly.
It says it sent an email to anybody who was booked on a flight up to and including Wednesday 20 September which has been cancelled but it has not said when people are booked to travel after that date will be notified.
The Irish Travel Agents Association has called on the airline to publish a full list of the flights to be cancelled over the next six weeks.
Ryanair says anybody who was booked on a cancelled flight can avail of a full refund or travel on a later flight.
In a statement issued this morning, Ryanair said: "Flights are operating as scheduled unless an email confirming a cancellation has been received."
It added: "We advise customers to check the email address used to make their booking.
"Cancellation notices for flights cancelled up to and including Wednesday 20 September have been sent to affected customers and we will continue to send regular updates.
"We will cancel 40 to 50 flights daily for the next six weeks, (less than 2% of our schedule) with a slightly higher number this weekend as we begin to implement these cancellations.
"Flights are operating as scheduled unless an email confirming a cancellation has been received. We advise customers to check the email address used to make their booking.
"Cancellation notices for flights cancelled up to and including Wednesday 20 Sept have been sent to affected customers and we will continue to send regular updates and post flight information on our website. We apologise to all affected customers for these cancellations.
"We have messed up in the planning of pilot holidays and we're working hard to fix that."
Ryanair has published a list of the flights it has cancelled tomorrow.
It includes eight flights to and from Dublin Airport. No other Irish flights are on the list
The Dublin flights are as follows:
FR 3103 Amsterdam-Dublin
FR1948 Dublin-Frankfurt Hahn
FR1949 Frankfurt Hahn-Dublin