The company said air traffic control (ATC) delays and strikes, bad weather and a backlog of annual leave to be taken by pilots and cabin crew had led to punctuality falling to below 80% over the last two weeks.
A spokesman said this figure was “unacceptable” and reducing 2% of scheduled flights until the end of October would help improve performance and allow staff to take holiday.
The airline apologised to affected customers, who it said will be offered alternative flights or refunds.
But passengers took to social media to complain to the company.
Some customers said last-minute cancellations had left them out-of-pocket due to non-refundable accommodation costs, or with no choice but to book expensive alternative flights or transport.
Others said they had been left stranded in their holiday destination.
Many urged Ryanair to publish a list of all flight cancellations.
Writing on the airline’s Facebook page, Maria Joanna Suquitana said guests travelling to Italy for her brother’s wedding had their flights cancelled just hours before they were due to depart.
She wrote: “We were forced to rent a van from Germany and drive 16 hours because we just can’t trust to fly with you again. Most stressful days of our lives.”
Karen Naughton Brill said her daughter’s 21st birthday present of flights to Amsterdam had been “ruined” when they were cancelled with less than 12 hours notice.
She wrote: “S he’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.”
Olivia Poole said her flight on Sunday was cancelled “with no explanation”.
She wrote: ” We’ve shelled out five times our original flight price for last minute, incredibly overpriced flights with another airline as your next available flights were on the day we’re due to fly back. I will be going to any length required to receive the compensation as per EU legislation.”
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. So customers have enough time to make alternative plans. Ryanair it’s wrong to leave people in suspense at the last minute. It’s not fair.”
Ryanair said a change in the company’s holiday year, from April to March to a calendar year from January 1 2018, had seen an increase in holiday allocations as staff used their annual leave before the end of the year.
It said the 40 to 50 flight cancellations each day accounted for less than 2% of its 2,500 daily flights and it would create additional standby aircraft to help restore punctuality.
Robin Kiely, head of communications at Ryanair, said: “We have operated a record schedule and traffic numbers during the peak summer months of July and August but must now allocate annual leave to pilots and cabin crew in September and October while still running the bulk of our summer schedule.
“This increased leave, at a time of ATC capacity delays and strikes, has severely reduced our on-time performance over the past two weeks to under 80%. 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%.
“We apologise sincerely to the small number of customers affected by these cancellations and will be doing our utmost to arrange alternative flights and/or full refunds for them.”