The airline, which flies to more than a dozen destinations from Leeds Bradford, says staff need to catch up with holiday entitlement.
Punctuality has fallen below 80 per cent in the first two weeks of September, it said, "through a combination of air traffic control capacity delays and strikes, weather disruptions and the impact of increased holiday allocations to pilots and cabin crew as the airline moves to allocate annual leave during a 9 month transition period (April to December 2017) to move the airline’s holiday year (currently April to March) to a calendar year (Jan to Dec) from 1st January 2018 onwards”.
It claims less than two per cent of flights will be cancelled, but passengers have expressed their fury over late cancellations.
No Ryanair flights from Leeds Bradford appear to have been cancelled today, with departures to Venice, Dublin and Chania getting underway this morning.
However many passengers have had their plans left in shreds.
Olivia Poole said on Facebook: "Complete lack of sensitivity, common sense and respect. No words. We've shelled out 5x 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 (LOL). I will be going to any length required to receive the compensation as per EU legislation.
"Changing your annual leave scheme = unforeseen circumstances beyond your control? Don't think so!"
Another Helen Bell said: "So they say it only affects 2% of their customers. Rubbish it affects 100% of customers for the next 6 weeks worrying if their flight will be cancelled. It's just ridiculous."
Ryanair has told customers flights are operating as scheduled unless they receive emails saying otherwise.