Kiely cited air traffic control (ATC) delays and strikes, weather disruption during the summer, and a backlog of crew leave before the end of the year as reasons for the decision.
It said: "If you have been affected by the Ryanair programme of flight cancellations you are entitled to a choice of refund or rerouting".
The airline is moving the airline's holiday year from an April to March calendar year to a January to December one.
Customers have taken to social media to complaining about their treatment, with some saying they were unable to cancel a hotel booking and left out of pocket.
Facebook user Harriet Kathryn Ross wrote: "What they need to do is confirm and publish a schedule of which flights will be cancelled over the next six weeks". Most stressful days of our lives'.
The only flight alternative offered by Ryanair was a Monday flight, which was the date he was originally scheduled to return back to Leeds.
She wrote: "She's gone to bed in tears, rang hotel, can't get refund too short notice, same with parking, Anne Frank house tickets etc etc all non-refundable".
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Ryanair have issued an apology to the public after they announced that they would cancel 50 flights over the next few weeks.
Passengers on affected flights will receive a text message or email, Ryanair said.
"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".
"Ryanair apologises sincerely for the inconvenience caused to customers by these cancellations".
"We are sorry and it's because we messed up pilot holiday planning and are working hard to fix".
Through cancelling fewer than 2% of the flights during the upcoming six months, or until the winter schedule begins, we will succeed in improving the resilience of operations for scheduling and restore the annualized target goal of punctuality of 90%, said a Ryanair spokesperson.
"Ryanair's on-time performance has declined from 90% to under 80% over the past two weeks, a figure that is unacceptable to Ryanair and its customers", it says.