Aer Arann is to suspend it services from Cork to Dublin and Belfast from the end of next month.
The Irish carrier currently operates one return flight a day, except Saturdays, from the southern Irish city to the two capitals.
The same aircraft, a 48-seat ATR-42 is used on both routes but Aer Arann said it has to be returned as its leasing agreement has ended.
The two services will end on August 31 but the carrier said it remained committed to Cork.
Andrew Kelly, Aer Arann's corporate affairs director, said: "We sincerely regret having to suspend these services and the inconvenience that it will cause our loyal customers on both routes.
"Unfortunately however we have an aircraft leaving the fleet and this has an obvious but regrettable impact on our schedule".
Aer Arann said all passengers booked on the flights after August 31 would be refunded.
www.aerarann.com