In Italy, where Ryanair carries more passengers a year than any other airline, the antitrust agency is now looking into whether it has violated consumers' rights.
"We make mistakes", he said.
"We expect to have the vast majority of these completed by the end of this week".
The low-priced carrier said last week it would cancel as many as 50 flights a day until the end of October after misallocating pilot holiday until the end of the year.
The bill for the compensation for passengers left stranded and forced to re-book during the current flight cancellations could reach €20million (£17.7 million).
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Ryanair had offered captains a one-off payment of GBP12,000 or EUR12,000 and first officers GBP6,000 or EUR6,000 to work extra days to alleviate the impact of the airline's cancellation of 2,100 flights over the rest of September and through October.
"Every day there are vacancies advertised with attractive packages attempting to entice pilots to relocate to Asia, and in some cases even allowing pilots to be based locally at home", says OAG's latest blog. "There isn't a union".
"The pilot market is changing, and Ryanair will need to change the ways which the pilots and management work together to ensure a stable and common future for everyone", the pilot representatives said in the letter.
Ryanair said it was preparing for up to €20m in compensation claims and €5m in lost fares as a result of the cancellations, although analysts estimated the total cost could be higher. "It seems clear that Ryanair has failed to plan properly for the implementation of the regulations".
The airline said the cancellations were brought about by the over-allocation of pilots' holidays during a relatively busy period.
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Loizos Heracleous, a professor of strategy and organization at Warwick Business School, said it is surprising that a company so focused on optimizing operations "could be caught out like this", and that it is mushrooming into a much bigger problem.
Also on Thursday, SkyNews reported that Ryanair plans to hire 125 new pilots in the next week or two as it faces the pilot shortage.
There are reportedly many employees on the verge of abandoning Ryanair for other airlines in Europe - which would add to the current flight cancellation chaos.
Separately, some Ryanair pilots have spoken to the BBC about a "toxic" atmosphere and how they felt "undervalued".
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