Airline boss had accused employees of being precious and full of their own self-importance after company was forced to scrap thousands of flights

The Ryanair chief executive, Michael O’Leary, has issued an unprecedented apology to his pilots in an attempt to stem the crisis at the Irish airline, which has cancelled thousands of flights and faced the threat of an employee revolt.

The airline had to scrap the bookings of more than 700,000 passengers last month due to an apparent shortage of pilots, having failed to plan for enough leave for staff.

Ryanair hoped a bonus payment could entice some pilots to change their holiday plans, but O’Leary then further inflamed the situation with disparaging comments about pilots at the airline’s annual meeting in Dublin.

On Thursday, the outspoken boss sent an extraordinarily contrite letter to pilots at the airline “to apologise personally to each of you for the disruptions you have experienced”.

O’Leary had accused pilots of being “precious about themselves” and “full of their own self-importance”, adding: “I would challenge any pilot to explain how this is a difficult job or how it is they are overworked, or how anybody who by law can’t fly more than 18 hours a week could possibly be suffering from fatigue.”

He said that the comments had been directed at “pilots of competitor airlines and their unions”, a favoured refrain of O’Leary’s when addressing those who have criticised his employment model. “I have the utmost respect and admiration for Ryanair’s pilot team,” he said.

The letter offered a range of improvements to terms and conditions, including salary increases, loyalty bonus payments, improved rostering and better compensation for those pilots forced into working away from their home base.

But it warned pilots against taking alternative employment with other airlines, particularly Norwegian, where hundreds are thought to have decamped. A graph of his rival airline’s tumbling share price, along with some choice financial facts, was appended to the letter. O’Leary warned earlier this year that Monarch, which collapsed into administration this week, and Norwegian would not survive the winter.

The letter, however, showed that the airline’s management is extremely conscious of the extent of pilot anger. O’Leary warned that he would stick with Ryanair’s “employee representative committees”, the forums it claims do the job of unions, which it refuses to recognise. He said the committees would be the only way to negotiate better pay and warned pilots “you and your colleagues will suffer” if they were ignored.

Pilots around Europe are unofficially organising, with many seeking union recognition. Ryanair staff in the UK hope to come together to halt its practice of negotiating individual deals with bases.

A number of pilots remain under tax investigation after working for Ryanair through one of its intermediaries, which instructed them to form companies as effective self-employed contractors – a practice which has attracted the attention of authorities around Europe. About half of Ryanair pilots are not officially employed by the airline.

The Civil Aviation Authority has pledged to monitor Ryanair’s treatment of passengers in the wake of the mass flight cancellations, after giving it an ultimatum to finally inform disappointed customers of their full rights or face legal action.

• This article has been amended to correct a misspelling of “jibes” in the headline.