Ryanair has said that 98% of customers hit by flight cancellations in September and October have been refunded or transferred to alternative flights or transport.
The airline has faced heavy criticism after scrapping thousands of journeys, blaming an error over pilot holiday rotas.
It initially said last month that 2,100 flights would be cancelled in September or October – or as many as 50 a day.
In a further blow to passengers last week, an additional 18,000 flights for the winter season were scrapped.
Ryanair reiterated its apology to customers in its latest trading update.
Chief marketing officer Kenny Jacobs said: “We have now re-funded/re-accommodated 98% of customers who were impacted in September and October.”
He said the remaining 2% had yet to contact the airline.
The update came as Ryanair published September traffic figures showing passenger numbers grew 10% to 11.8 million in September.
Video: Ryanair capitulates and promises not to mislead customers
Andrew Haines, head of the Civil Aviation Authority (CAA), last week said he was “furious” with the low-cost carrier, saying it appeared to show “disregard for consumers and for the law”.
The CAA accused the Dublin-based group of not complying with the law over its handling of the cancellations.
It said Ryanair had not told customers about European rules meaning they were entitled to be re-routed by another carrier.
The airline has since emailed customers, informing them of their rights to receive a refund or be transferred on to other flights or travel by train, bus, or hire car.
However, it has also complained that British Airways was not held accountable in the same way when an IT meltdown stranded 75,000 passengers in May.
Ryanair customers have expressed frustration after many were left out of pocket due to a lack of alternative flights and accommodation bookings they can no longer use.