Cityjet has confirmed it will cancel its Cardiff routes to Edinburgh and Paris on June 29.
The airline has blamed the airport's decision to allow Flybe to establish its own competitor routes to the two cities for the cutbacks, reports walesonline.co.uk.
Earlier this year, Flybe announced it would open a base at Cardiff airport, serving 11 destinations, this summer.
The move has resulted in Flybe offering "almost identical" flight timings to Edinburgh and Paris as those provided by Cityjet.
Cityjet CCO Cathal O'Connell has hit out at Cardiff airport for "favouring" Flybe and has announced his airline will cease operating its Edinburgh and Paris routes next month.
He said: "Both business and leisure interests in Wales welcomed us to Cardiff in January 2014 when these routes were abandoned by the previous operator.
"Since then we have carried over 100,000 customers on these services. We have invested in building our presence in the marketplace, including the upgrading of the aircraft from a 50-seater to 70-seater in March this year and the establishment of a crew base at Cardiff by Stobart Air, who operate the services on our behalf.
"We can fully understand the desire of the airport to build its network. What we cannot accept is Cardiff airport enticing another airline to provide service on a bundle of routes which include two routes already operated by Cityjet from Cardiff.
"The fact that the other airline's flight timings are almost identical to Cityjet's questions what benefit Cardiff airport management sought to achieve from this venture.
"Competition is not a problem, but competition should be based on a level playing surface and not one where an airport clearly favours one airline over others."
Debra Barber, managing director of Cardiff airport, said: "After 18 months of operations, we are naturally disappointed that Cityjet has decided to stop flying services from Cardiff to Edinburgh and Paris."