Ryanair's Kenny Jacobs said: 'We will cancel 40 to 50 flights daily for the next six weeks, (less than 2% of our schedule) with a slightly higher number this weekend as we begin to implement these cancellations.
The low-priced carrier was prompted to take the drastic step after seeing less than 80 per cent of its planes arrive on time in the first two weeks of September.
The airline says it regrets this and is working hard to fix the problem, and to make sure it doesn't happen again.
In a statement, the airline said: "These tighter crewing numbers and the impact of ATC capacity restrictions in the UK, Germany and Spain, as well as French ATC strikes and adverse weather (thunderstorms) have given rise to significant delays in recent weeks".
If the airline cancelled 40 flights per day for six weeks at a load factor of 90%, approximately 285,000 journeys would be affected.
While a cut of between 40 and 50 flights per day sounds like an extreme measure, it is worth noting this represents just 2% of the 2,500 flights it operates every day.
Changes imposed by the Irish Aviation Authority in line with European law means Ryanair must bring staff holidays in line with the calendar year from January, requiring it to allocate that leave before the end of the year.
Passengers affected will be offered alternative flights or refunds, Ryanair said.
"We apologize 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", he said.
Following initial confusion among passengers on Friday, a Ryanair statement said its decision resulted from a need to "improve its system-wide punctuality which has fallen below 80 per cent in the first two weeks of September".
Karen Naughton Brill said her daughter's plan to celebrate her 21st birthday in Amsterdam was "ruined" when the flight was cancelled.
The move is also aimed at bringing punctuality back up to 90 percent by providing additional standby aircraft, after Ryanair's on-time performance fell below 80 percent in the first two weeks of September.
'Flights are operating as scheduled unless an email confirming a cancellation has been received.