The airline, which flies to more than a dozen destinations from Leeds Bradford Airport, says staff need to catch up with holiday entitlement.
"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".
Ryanair say the suspension of flights will affect around 285,000 passengers in the coming weeks ahead.
On social media, passengers expressed frustration at a lack of response from Ryanair as to specific flight cancellations.
Ryanair announced that fewer than 2% of all its flights would have to be cancelled and this move would help it to reach its annual target for punctuality of 90%. "Please check the email address used to make your booking".
"Cancellation notices for flights cancelled up to and including Wednesday September 20 have been sent to affected customers and we will continue to send regular updates".
Airline management says that due to these holiday period changes, Ryanair has been operating at record schedule and traffic levels during the peak summer months of July (12.6m passengers) and August (12.7m) which has now resulted in a huge backlog of crew leave.
It means that dozens of flights every day across Europe will be cancelled without warning leaving holidaymakers stranded.
If you were booked on a flight that has been cancelled, you might be eligible for flight compensation too.
If you are due to be flying with Ryanair over the next few weeks it would be sensible to check whether the flight is going ahead as planned.
It sent email notification to the first tranche of affected passengers on Friday, giving them the choice of a refund or an alternative flight.
More information on your rights as a passenger when your flight is cancelled is available here, but the rules for compensation are outlined on their website as below. Compensation may also be payable depending on the notice period Ryanair has given you.