Fullers is to stop ferry services to the suburbs of Half Moon Bay and Bayswater in Auckland within 90 days.
The company says it is facing big cost increases and is not getting the return on investment it is seeking.
Auckland Regional Transport Authority says the move is disappointing as both services are well patronised.
Other operators are now being approached about taking on the routes.
Fullers says rising fuel costs mean it is not commercially viable to continue to operate the two services.
The company says its contract for the two routes with the authority expired 15 months ago.
Chief executive Douglas Hudson says Fullers continued to run the services while working with the authority on a new contract. The authority offered an increased public subsidy, but it was not enough.
Mr Hudson says the authority refused to let Fullers raise the fares - despite a 60% increase in fuel costs.
