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The announcement comes just hours after a letter was sent to the company by a group of its existing pilots, rejecting an offer of a tax-free £12,000 bonus in exchange for working overtime, reports Sky News.
All 315,000 affected customers were emailed by Ryanair on Monday to advise them of flight changes, alternative flights, refunds and EU flight compensation law.
Just over 175,000 of those passengers will have been re-allocated different flights by the close of business on Wednesday, the Dublin-based carrier said.
It is also aiming to process 63,000 refunds by the end of the day.
The latest figures marked an improvement on last Friday when Ryanair shocked the travel sector with the proposed cancellation of about 2,000 flights in a move expected to hit an estimated 390,000 passengers.
The airline explained on Wednesday that there were fewer passengers affected because the number of bookings for October had fallen significantly.
"We apologise sincerely to each and every one of the 315,000 customers whose original flights were cancelled over a six-week period in September and October, while we work to resolve this short-term rostering failure," said marketing boss Kenny Jacobs.
"We have taken on extra customer service teams to speed up the rate at which we accommodate and action alternative flight requests or refund applications.
"We expect to have the vast majority of these completed by the end of this week."
However, passengers are reporting problems with the process of refunds or compensation for cancelled flights, saying the information supplied by Ryanair is incorrect and calls are going unanswered.
Ryanair estimates that the total cost will be as much as 25 million euros ($30 million) for the cancellations, which were sparked by the over-allocation of pilots' holidays during a relatively busy period.
Outspoken chief executive Michael O'Leary apologised to customers on Monday and admitted that the scandal would have a "large reputational impact" on the group.
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