Ten Flybe flights in and out of Belfast City Airport have been cancelled.
An industry-wide shortage of pilots was partially blamed for Wednesday's disruption by the company.
Flights affected include services to Birmingham, and round trips to and from Leeds Bradford Airport and Aberdeen.
A flight from East Midlands was also cancelled.
A statement by the airline said: "Flybe sincerely apologises to all our customers and partners affected by the current flight cancellations.
"Whilst 95% of Flybe flights are operating as per normal, we do recognise the impact of today's cancellations.
"We are doing our best to mitigate the impact of the current situation that has arisen due to a combination of factors including seasonality, pilots' end of leave year, Easter holidays, base restructuring and the shortage of pilots across the industry that Flybe has highlighted over recent months.
"We have already identified several mitigation actions and will be issuing further updates throughout the day.
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"All those affected have been emailed and advised they can re-book for travel on an alternative flight or apply for a full refund."
Passengers received texts and emails on Tuesday evening telling them of problems with their flights.
The disruption followed the launch of the airline's summer schedule.
Flybe was recently bought by the Connect Airways consortium, which includes Virgin Atlantic.
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