However, the pilots would not receive the bonuses until October of next year.
Ryanair will force pilots to delay planned annual leave as it battles to overcome shortages in coming weeks.
In the memo, Michael Hickey thanked those pilots who have already offered to operate during their month off.
The airline is cancelling 40 to 50 flights every day for the next six weeks, after it admitted it had "messed up" the planning of pilot holidays.
Balpa says Ryanair's problems have been exacerbated by the high turnover rate of pilots.
A source told Reuters that a letter had been approved by pilots at 17 of 85 Ryanair bases demanding new permanent, contracts under local labour law, though this could not be independently verified by Reuters.
In a bid to persuade pilots to work on their days off to ease the situation, it has offered captains a one-off payment of £12,000 and first officers £6,000.
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People who booked up with Ryanair can check the complete list of canceled flights on their website. The number of passengers affected is less than the initially announced 390,000, because September's preliminary reservations were 90%, compared with 70% in October, the company said. If these pilots refuse to work extra days, more cancellations and trouble could be on the way for the Irish airline.
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.
Mr O'Leary told the AGM that Ryanair was facing a "significant management failure" and the cancellations had cost the airline about 25m euros (£22m).
Today's cancellations are for flights to and from Berlin, Glasgow and Krakow.
When asked about reports the pilots were threatening industrial action Mr O'Leary said: "If you want and need to ask your staff to give up holidays no work to rule can alter that".
Pilots are not treated as the highly trained professionals that they are by many companies and that is why they are leaving, according to a former member of the profession.
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