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.
A Tweet from Ryanair itself states that "Your flight is operating as scheduled unless you have received a cancellation mail".
"This has happened through a combination of ATC 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 nine month transition period".
"Ryanair's actions will also have a considerable impact on route schedules internationally where many travellers are dependent on their Ryanair flight to connect to onward worldwide flights".
However, passengers have taken to social media to express their anger, with some of them left stranded overseas. Rubbish it affects 100% of customers for the next 6 weeks worrying if their flight will be cancelled.
She said: 'She'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'.
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. "I will be going to any length required to receive the compensation as per European Union legislation".
She wrote on Facebook: 'We were forced to rent a van from Germany and drive 16 hours because we just can't trust to fly with you again. Ryanair it's wrong to leave people in suspense at the last minute.
Throughout the day on Friday, the Ryanair Twitter feed was filled with complaints from passengers who had their flights cancelled, with one describing the lack of notice an "absolute disgrace" and another saying it was "shocking".
The airline stunned passengers by cancelling up to 2,000 flights over the next six weeks, in order to give crew some time off.
Ryanair's head of communications, Robin Kiely said: "We will be doing our utmost to arrange alternative flights and/or full refunds".
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.