Rotorua was 14 minutes' flying time from Tauranga, 18 minutes from Taupō and 26 minutes from Hamilton.
"I accept that there will be some unease in Rotorua about this change. To reassure the community that it will continue to receive a consistent, quality service a new clinical oversight group will be created to monitor the impact of these changes," Clark said.
Rotorua and Taupō residents fought hard to have the local helicopter services included in the tender process for the rejigged rescue service, with marches and public meetings revealing the level of local concern.
The Government agreed to include services based in the central North Island in the tender for air ambulance helicopter services after mayors from the region met Clark in April.
The Philips Search and Rescue Trust operates rescue helicopters at six bases in the North Island, including the BayTrust Rescue Helicopter servicing Rotorua and Bay of Plenty and the Greenlea Rescue Helicopter covering Taupo and the Central Plateau.
MP for Rotorua, National's Todd McClay, said the news was a massive blow to the people of Rotorua.
"Health Minister David Clark has said that there will be no change in response times, but that simply doesn't make sense when helicopters will have to travel from other centres.
"The people of Rotorua deserve to have their own rescue helicopter service and they shouldn't have to rely on choppers coming from Taupo, Tauranga and as far away as
Hamilton," McClay said in a statement.
Clark said today's announcement, the second in principle agreement for air ambulance services, was a key part of an improved national service and followed a recent announcement covering Auckland and Northland.
An announcement on the South Island service will be made later this month.
"Modernising our air ambulance services is a major undertaking and the Government invested an extra $82.9 million over four years into these services in the 2018 Budget. These changes will deliver a safer, better service that is firmly focused on patients," Clark said.
It is part of a 10-year programme to increase crew numbers, reduce callout times and ensure all air ambulance helicopters are twin-engined, allowing more space to treat patients while in the air.
Rescue helicopter services are generally funded around 50 per cent by the Government and 50 per cent by the community via sponsorship and donations.