Ryanair's chief operations officer is to leave the airline at the end of the month, the first executive to go since the cancellation of tens of thousands of flights because of staffing issues.
Michael Hickey (centre) is leaving Ryanair.
Addressing comments he had made about pilots after the company's AGM last month, Mr O'Leary said Ryanair's pilots were the best in the business, worked hard, were well trained and were extremely professional.
Mr O'Leary's apology came after he accused the pilots of being "full of their own self-importance". The Guardian reports that HMRC are investigating Ryanair pilots over the company's tax structure and use of Irish limited companies to employ UK-based pilots in order to avoid paying sick pay and other benefits.
O'Leary has previously apologised publically for the changes in the rota - brought about to comply with new aviation rules - which led to a shortage of pilots because the airline failed to plan for enough leave.
On Thursday, he sent an unusually contrite letter to pilots at the airline "to apologise personally to each of you for the disruptions you have experienced".
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No response has yet been made public from Ryanair's pilots or unions who now represent a portion of them.
The operating chief, who assumed the post in 2014, has been at the airline since 1988, joining as an engineer and rising to direct the department.
More than 700,000 passengers' travel plans have been affected by what Ryanair boss Michael O'Leary admitted was a "cock up".
At the end of September announced that the winter will cancel another 18 thousand flights.
It was then forced to improve its compensation to passengers after the airline came in for criticism from the Irish Commission for Aviation Regulation (CAR) over its handling of the crisis, and for not advising passengers fully of their rights.