A Ryanair plane at Dublin airport. Paul Faith/AFP/Getty Images

Ryanair has contacted the passengers who were affected by its flight cancellations and schedule changes until March, in order to explain their entitlements under EU261 regulations.

The Civil Aviation Authority had given the Irish carrier until 5pm on Friday (29 September), to arrange compensation for the 700,000 passengers affected by the 2,100 flights cancelled between September and October and the 18,000 schedule changes between November and to March 2018.

The airline said customers will be able to choose between a full refund option or a re-routing option. Should passengers opt for the former, a full refund will be given of "an unused flight sector and associated fees". If the disrupted flight is their outbound sector, customers will also be offered a full refund of the return sector.

Should passengers opt to be re-routed instead, Ryanair will offer them to be moved on the next available flight on the same route.

Should the option be unavailable on the same or next day, the Irish carrier will either move passengers onto the next available Ryanair flight from/to a suitable alternative airport, such as London Luton or London Gatwick for flights that were scheduled to depart from London Stansted.

However, should re-routing passengers on flights from/to different airports not be available on the same or next day, customers will be offered the option of travelling on Easyjet, Jet2, Vueling, Cityjet, Aer Lingus, Norwegian or Eurowings flights to their destination.

Under EU261, Ryanair will also reimburse any reasonable out of pocket expenses incurred by customers as a result of these flight cancellations, subject to receiving an EU261 expense claim form from customers supported by original receipts.

The airline added that any affected customers who believe they may have chosen an option that was not suitable for them as a result of any misunderstanding of their EU261 rights, should directly contact Ryanair's Director of Customer Services.

"We apologise again sincerely for the disruption and inconvenience our rostering failure has caused some of our customers," said Ryanair marketing director Kenny Jacobs.

"Over the past week we have refunded/reaccommodated over 97% of the customers affected by the 18 September cancellations.

"We have restored the reliability and punctuality of our flight operations. Over the past seven days we have operated over 15,000 flights with over 96% of our first wave morning departures operating on time, or with zero flight cancellations."

The Dublin-based airline announced it would cancel a further 18,000 flights between November and March. It added 34 routes will be affected by the temporary winter suspension, including London Stansted to Glasgow and Edinburgh, London Gatwick to Belfast, Newcastle to Faro, and Glasgow to Las Palmas.

The move will affect approximately 400,000 passengers and comes two weeks after a shortage of pilots forced the carrier to cancel between 40 to 50 flights a day until 31 October, affecting approximately 315,000 passengers across 2,000 flights.

The issue stemmed from Ryanair's decision to reschedule its holiday year to run from January to December, rather than the current system, when it runs from April to March. As a result, it had to allocate annual leave to pilots in September and October.

That, coupled with weather delays and air traffic control strikes, left the airline with no other option than to cancel 2% of its flights up until the end of next month and forced O'Leary to admit the airline had "messed up".