The Civil Aviation Authority has begun an enforcement action accusing Ryanair of "persistently misleading" some 715,000 passengers about their legal entitlements, according to its website.
The Taoiseach has said he expects Ryanair to ensure that passengers' rights are protected.
When asked if it would comply with the CAA's demands by the 5pm deadline, Ryanair said: "We will be meeting with the CAA and will comply fully with whatever requirements they ask us to".
Ryanair has more than doubled its unprecedented cancellations since last week, with cuts now affecting more than 700,000 customers over the next five months.More news: Thousands on the Indonesian island of Bali evacuated
Thirdly they must help all passengers who "chose an unsuitable option as a result of being misled".
Passengers affected by the new measure, "less than 1% of the 50 million customers we will transport this winter" received an email to inform about these changes and "offer alternative flights or total refunds".
Andrew Haines, chief executive of the CAA, commented: "There are clear laws in place, which are meant to assist passengers in the event of a cancellation".
If these options are not availabl, they state that they can then offer the customer re-accommodation by train, bus or auto hire "with the cost of this comparable transport ticket to be assessed on a case by case basis".More news: Saudi Arabia hands women the keys
The CAA did not say what action it would take if Ryanair did not comply, but it has the power to take court action against carriers that fail to comply with consumer rights laws.
The airline also confirmed that they will now compensate customers for any hotel costs or other expenses revolving around a cancelled flight as long as customers can provide receipts as proof.
RYANAIR announced that return flights between Dublin and Birmingham (FR 664 and FR 665), Paris Beauvais (FR 22 and FR 23) and Barcelona (FR 3977 and FR 3976) on Mondays between November and March will be cancelled.
He added that 99 per cent of Ryanair's customers remain unaffected by the cancellations.More news: Students Occupy University of Barcelona to Demand Independence Vote