Rotorua was the only regional centre to gain from the shake-up, with a boost to capacity between Auckland and Rotorua from next February.
Air NZ will introduce the larger Bombardier Q300 aircraft on the Rotorua route, replacing the Beech 1900D on weekday morning services, which would increase the total seat capacity by 30 percent.
The airline said the recent introduction of new ATR72-600 aircraft had enabled it to free up Q300 capacity for the Auckland-Rotorua route.
It said the cost advantage of operating larger Q300 aircraft over the smaller Beech 1900Ds increased the economic viability of the route.
Air NZ said significantly more seats would be available at the lead-in fare level of $79 one-way.
The end of Wairarapa services has come as a devastating blow to the Masterton and Carterton councils, which invested more than $1 million in airport facilities at Hood Aerodrome.
Eagle Air, the Air New Zealand subsidiary, began operating between Masterton and Auckland in February 2009 and up to March 31 this year had undertaken 528 flights carrying 6927 passengers, averaging 13 per flight, according to Masterton District Council.
It and Carterton District Council, with assistance from the Wairarapa Building Society and Trust House, upgraded the taxiway, lighting, terminal building, carpark and services.
Air New Zealand's regional affairs manager Ian Collier and general manager network Richard Thomson travelled to Masterton today to break the news.
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.
He said Air New Zealand had previously told him the service was only marginally profitable but would continue.
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, Mr Daniell said.
"Air New Zealand has confirmed its willingness to respond and cooperate with this group.''
Destination Wairarapa general manager David Hancock said it had 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.''
Mr Hancock said while it was disappointing news, Destination Wairarapa respected that this was a commercial decision.