More than 50,000 passengers have been affected at the peak of the summer holidaying season, but Ryanair say they aren't due compensation because the unions have acted "unreasonably".
However, the Civil Aviation Authority said passengers "have the right to seek compensation under European Union legislation when flights are delayed by three hours or more, cancelled or when they are denied boarding".
The pledge comes less than a year after the CAA threatened Ryanair with legal action over it handling of compensation claims when thousands of flights were cancelled following mismanaged holiday rotas for its pilots.
The Irish low cost carrier - Europe's largest by passenger numbers - is in the midst of its worst week of stoppages in more than three decades of flying, as it struggles in talks with trade unions who it has chose to recognise for the first time.
"If our reputation for reliability or forward bookings is affected, then base and potential job cuts such as these at Dublin are a deeply regretted outcome", Ryanair's chief operating officer Peter Bellew said in a statement.
'Under EU261 legislation, no compensation is payable when the union is acting unreasonably and totally beyond the airline's control'.
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Meanwhile, a second day of strikes by Ryanair cabin crew is under way in Spain, Portugal and Belgium.
EU Regulation 261 entitles passengers to payouts of €250 (£222) when short-haul flights are cancelled without a fortnight's notice, in addition to refunds or new flights - but Ryanair are standing firm.
"All 3,500 affected customers have already been notified by email/SMS earlier today and will be readily re-accommodated (or refunded) on other Ryanair flights between Ireland-UK routes".
Airlines can only avoid this payment under the EU261 system when the cancellation is caused by "extraordinary circumstances" beyond the carrier's control - including extreme weather incidents and strikes by air traffic controllers.
The union feels that no progress has been made regarding the issue which led to Fórsa recently announcing that some of their Irish-based Ryanair pilots will be taking industrial action on 3 August.
Europe's top court ruled in April that airlines have to pay compensation for delays caused by wildcat strikes that result from management decisions.