Kenny Jacobs, chief marketing officer, said the company was "working hard to fix" the problem, after it announced a 2% reduction in scheduled flights until the end of October.
He said: "We apologise to all affected customers for these cancellations. We have messed up in the planning of pilot holidays and we're working hard to fix that."
Ryanair 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 the company has apologised to affected customers, who it said will be offered alternative flights or refunds.
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 and m any 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."
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."
"In the event of any disruption or cancellation airlines must ensure customers are fully compensated and every effort is made to provide alternative travel arrangements."