The airline said it will email customers affected with offers of alternative flights or full refunds, and details of their EU261 compensation entitlement.
The budget airline cancelled 82 flights yesterday (Sunday, September 17) and is expected to scrap up to 2,000 more over the next six weeks.
Services from Dublin to London Gatwick and Amsterdam, along with flights from Brussels and Manchester to Dublin are among 12 Irish flights cancelled by the under-fire airline today.
One user said she feared for her wedding, with 30 Ryanair flights booked for her party, while others said that even if their outbound flight was not cancelled, they could not be sure if their inbound flight would be.
Passengers whose flights have been cancelled by Ryanair are being advised of their rights by the Commission for Aviation Regulation.
Ryanair's Marketing Officer Kenny Jacobs said affected customers with bookings up to 20 September have been informed.
It has furnished a list of affected flights up until Wednesday, but so far Shannon flights aren't affected.
So why is Ryanair cancelling its flights?
"This increased leave at a time of ATC capacity delays and strikes (in France), has severely reduced our on-time performance.to under 80 percent", he said.
Ryanair boss Michael O'Leary
"By cancelling less than 2% of our flying programme over the next six weeks - until our winter schedule starts in early November - we can improve the operational resilience of our schedules and restore punctuality to our annualised target of 90%", he added.
O'Leary confirmed a report in the Irish Independent that Ryanair had been offering some pilots a 10,000 euro ($11,925) "signing-on bonus" to keep up with its rapid passenger growth.
Ryanair blamed a number of factors for the sudden cancellations including a backlog of staff leave, which must be taken by the end of the year.
It must also honour its legal duty to arrange alternative flights or provide a full refund, inform passengers of their rights and proactively pay compensation and reimburse reasonable out of pocket expenses.
That means around 2,000 flights cancelled and around 400,000 passengers affected. In most cases Ryanair will offer you another flight with them.
Firstly, the company changed its holiday year from January to December rather than April to March.
If Ryanair has informed you of the cancellation with more than two weeks' notice, you will not be entitled to compensation. "I say we want to put our hands up, which is what we do when we make a mess", O'Leary told a news conference.
Air passengers can also claim compensation for cancelled flights, ranging from anywhere between €250 to €600 depending on the duration of the flight.
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