The budget airline has angered travellers after announcing plans to axe between 40 and 50 flights per day until the end of October.
Up to 400,000 Ryanair passengers will have their holidays and travel plans ruined as a result.
And today the European Commission urged Ryanair to comply with EU passenger rights, including possible compensation.
Under Brussels regulations, passengers can claim up to £529 (€600) if their flights are cancelled with less than two weeks’ notice.
A European Commission spokesman told a press conference in Brussels: “Airlines operating in the EU need to respect the European rules.
“Passengers whose flights are cancelled have a comprehensive set of rights. 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.”
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.
The airline also said air traffic control strikes and weather disruption were affecting its performance.
And rival Norwegian Air has recruited more than 140 pilots from Ryanair this year, adding to the squeeze on staffing.
Ryanair said the cancellations were designed “to improve its system-wide punctuality which has fallen below 80 per cent in the first two weeks of September”.
Michael O’Leary, Ryanair’s chief executive, has said every passenger who is entitled to compensation will receive it in full.
He said: “It is clearly a mess but in the context of an operation where we operate more than 2,500 flights every day, it is reasonably small.
“But that doesn’t take away the inconvenience we’ve caused to people.”
The Commission for Aviation Regulation in Ireland said it is working with Ryanair to solve the issue.
Commissioner Cathy Mannion told RTE: “They fully accept that they have to pay up all the rightful compensation claims and all the care and assistance.
“If Ryanair have cancelled your flight, they must offer you an alternative flight at the earliest opportunity or refund your ticket.”