The airline cancelled 82 flights on Sunday and added it will cancel between 40 and 50 flights a day for the next six weeks after messing up holiday schedules.
The BBC has reported marketing officer Kenny Jacobs said customers with affected bookings up to September 20 have been contacted over the issue.
He added: "We have messed up in the planning of pilot holidays and we’re working hard to fix that."
The problem has emerged following a backlog of staff accrued which meant many Ryanair workers have booked their holidays towards the end of the year.
The airline has also changed its holiday year from April to March to January to December which has meant allocating annual leave to pilots in both September and October.
Passengers whose flights have been cancelled are being offered alternative flights or refunds.
The airline added less than 2% of its flights would be cancelled and the move would help it hit its annual punctuality rate of 90%.