Aer Arann, which operates as Aer Lingus Regional, is to terminate its services at Waterford Airport from 6 January.
The routes affected will be Aer Lingus Regional services from Waterford Airport to London Southend, London Luton and Manchester.
The airline said that passengers with bookings for flights after 6 January will be contacted directly in the coming days.
It said all passengers will be re-booked on alternative Aer Lingus Regional flights or given a full refund.
All Aer Arann employees at Waterford Airport will be redeployed in the company.
The airline said it will continue to offer services to London Southend from Dublin Airport and to Manchester from Cork and Shannon airports.
The airline, which is currently concluding a strategic growth plan, described the suspension of services from Waterford as ''regrettable but necessary''.
''We are in the process of finalising a new business plan that will put the airline on a path for growth,'' said Sean Brogan, interim chief executive at Aer Arann.
''We have worked hard to overcome recent challenges, built a successful new partnership with Aer Lingus and grown our passenger numbers. If we are to protect and nurture these gains, we have got to concentrate resources on services that offer sustainable returns,'' he added.