The airline has been forced to cancel up to 50 flights a day for the next six weeks because of a mix-up in holiday leave for its pilots.
Michael O'Leary has revealed that Dublin-based pilots are getting a pay rise, and it will be offered to staff at some other bases too.
But one group, made up of employee councils from 14 Ryanair bases across Europe, have sent a letter to the firm refusing the offer.
O'Leary refused to discuss media reports that many pilots had turned down offers of a €12,000 bonus and instead demanded improved contracts.
He added the company does not need the agreement of pilots to take back a week of leave and added that if pilots "misbehave there will be no goodies".
He admitted "significant management failure" regarding the rostering of pilots, and warned that the moves would not guarantee an end to disruptions.
He dismissed talk of possible industrial action, including reported plans for a work-to-rule, saying: "There isn't a union".More news: Arsenal vs Cologne — UEFA Europa League
The bonuses would be conditional on completing more than 800 flight hours for Ryanair in the 12 months up to 31 October 2018.
Former Ryanair pilot James Atkinson, writing in the Guardian, said the airline uses divide and control tactics to keep pilots on different kinds of contracts and to prevent them from organizing.
Alex Neill, managing director of home products and services, said: "It's outrageous that Ryanair passengers who have had already to endure huge inconvenience are essentially being double charged for booking seating and luggage".
The current crisis is being officially blamed on pilot holidays but details have been emerging of an exodus of crews to other budget & low-priced airlines such as Norwegian and Jet2 who operate the same type of aircraft as Ryanair.
"If Norwegian Air are holding open days, there's nothing we can do, despite the fact that we have very good terms and conditions".
"There's an underlying problem at Ryanair, which is quite simply that the company can not replace pilots as fast as they quit", he wrote.
Ryanair has said it expects to have re-accommodated more than 95% of the 315,000 customers affected by cancellations by end of this week.