The country's air navigation service provider - Airways New Zealand - is proposing to remove services from seven regional airports around the country.
Rotorua, Napier, New Plymouth, Gisborne, Invercargill, Kapiti Coast and Milford Sound airports may all lose their air traffic services.
Air Line Pilots' Association's president Captain Andrew Ridling told Morning Report regional airports that don't have control towers already don't have A320 jet engine aircraft or ATR aircraft flying in.
"Removing these control towers from, must be a third of New Zealand's airports, puts in jeopardy our whole safety system we have in the first place. That's why we have air traffic control."
He said in Rotorua, there are a range of activities happening below the flight path like tourist helicopters and skydiving.
A lot of public money has already been spent to keep airways safe in the future, he said.
"I'd suggest that the regional airlines and where these towers are scheduled for closure will probably be the first to come back to the usual schedule because they're the ones that actually need service."
Once they're gone there's no way they can come back, he said.
Air Line Pilots' Association's president Captain Andrew Ridling speaks to Morning Report
Chief executive of Airways New Zealand Graeme Sumner says "it's just not true" that it's unsafe.
The industry is going through enormous pain at the moment, he said.
"I think it's responsible to take out costs where safety is not compromised and it's clear that in this case we can do that," he said.
"The industry has been devastated and I would want to correct the view that we can't come back in the event that volumes increase but realistically that's going to be some time away."
"It's just not true" - Graeme Sumner
He said Air New Zealand have been very supportive of the proposal.