Air New Zealand's regional affairs manager Ian Collier and general manager network Richard Thomson came to Masterton today to break the news.
Mr Thomson said they had reviewed regional services, and the Masterton operation had reached a point where a decision needed to be made.
"The service is not economically sustainable,'' he said.
Mr Collier acknowledged it was "obviously hugely disappointing. We recognise the effort the local communities put in to support the services, we're very grateful for that.''
He said they would continue to work with the community to look at alternatives.
The pair later drove to Wanganui, to announce the loss of the Wellington-Wanganui service from December.
Masterton mayor Garry Daniell said the service was a wonderful asset to the Masterton people.
Air New Zealand had previously told him the service was only marginally profitable but would continue.
"After strong community support for both the development of infrastructure at Hood Aerodrome, and good patronage at about 70 per cent - and recently increasing, Wairarapa representatives had been in active engagement with Air New Zealand do develop the service further.''
He said the council, in conjunction with Trust House and Destination Wairarapa, would form a working group to commence further discussion to determine what alternative services or aircraft could be put in place to maintain the route.
"Air New Zealand has confirmed its willingness to respond and cooperate with this group.''
Destination Wairarapa also said they thought Air New Zealand was committed to keeping the route.
"We are surprised and disappointed to hear this news, especially following all the feedback we've had from Air New Zealand to date suggesting that Wairarapa would be in Air New Zealand's fleet expansion plans and secondly following all the hard work we have been doing with Air New Zealand to grow the Auckland market,'' said Destination Wairarapa general manager David Hancock.
Mr Hancock said while it was disappointing news, Destination Wairarapa respected that this was a commercial decision.
The organisation would continue to work with Air New Zealand on service options for Masterton and other growth opportunities for the Wairarapa through Wellington and Palmerston North airports.