Air New Zealand will suspend all flights between Whanganui and Auckland, and Blenheim and Christchurch, at the end of July.
Both services were running at a loss, the company said, as not enough people were flying the routes.
Air New Zealand general manager of networks, Richard Thomson, said since Jetstar began flying from Palmerston North - just 70 kilometres from Whanganui, the market dynamics had changed.
"The greater number of destinations, higher frequency of service and wider range of connecting options on offer at [Palmerston North] airport have unfortunately served to undermine demand for Whanganui services.
"We've seen customers effectively voting with their feet and using Palmerston North rather than Whanganui Airport."
To fly from Auckland to Whanganui on Tuesday with Air New Zealand, the cost is $299.
To fly with the airline to Palmerston North, prices start at $149. Jetstar does not fly to Whanganui, but a flights to Palmerston North tomorrow start at $45.
"Despite almost halving the average fare on this route we've been unable to create sufficient additional passenger volume to sustain an ongoing service and unfortunately this means we will cease operating to Whanganui," Mr Thomson said.
Whanganui airport is a joint venture, owned in equal partnership by the Whanganui District Council and Government.
Airport manager Allan MacGibbon said last week that Air New Zealand was its biggest customer "by far" in terms of landing fees.
Whanganui MP Chester Borrows called the decision "disappointing."
He was alerted to the decision last week, and said he was pushing fro Air New Zealand to make equipment and flight data at the airport available to other users.
"I believe passengers flying in to Whanganui should still be able to access their lounges including Koru Club for those Koru members. Flights should leave from Air New Zealand gates, so I'll be working to achieve that too," Mr Borrows said.
He said Air Chathams would take over the route from Air New Zealand.
Air New Zealand will also suspend its between Blenheim and Christchurch from July 31, as a result of insufficient demand.
Customers booked to travel on suspended services past July 31 will be offered the choice of a full refund or travelling via an alternative port.
Other changes to the national carrier's regional schedule include an earlier departure time of 7.10am for the first flight of the day from Whangarei to Auckland from October 30.
Also from that date, the first flight from Kerikeri to Auckland will depart on weekdays at 6.00am.
Northland MP Winston Peters said the new departure time from Whangarei was sensible, but the departure time from Kerikeri was "way too inconvenient."
Early morning Air New Zealand flights from Tauranga to Christchurch will be reinstated, departing 6.05am. The airline will also operate "up to 10" new weekly services between Auckland and Tauranga.