A Newshub investigation has uncovered multiple complaints about resourcing issues with the country's air traffic services.
A former air traffic controller says there are nationwide "systemic issues", and there are now concerns it could be impacting the safety of the traveling public.
The Dunedin air traffic tower was recently the subject of a Civil Aviation Authority (CAA) safety inquiry over an incident related to resourcing.
There have been complaints from controllers about resourcing in Wellington and Auckland, and over staff used to monitor air traffic above Raglan.
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"Our biggest concern is the staff resourcing right now," NZ Airline Pilots Association President Rim Robinson told Newshub.
"We know Airways NZ is only resourcing their staff levels at 95 percent of their required level, whereas they should be up around 105 percent.
"That's a public, a passenger safety concern," he added.
Newshub can reveal that since January last year, there have been 3872 occasions when air traffic control staff have been recalled to work on their days off.
"We would have thought Airways would have run an efficient call or reserve system to allow for sickness, but they don't," says Mr Robinson.
"They actually ask their staff to come back on their days off."
The company that provides air navigation services, Airways NZ, says it is sufficiently staffed - but accepts in some situations it's difficult to find cover. It says it operates at 99.8 percent service availability.
However, a former air traffic controller told Newshub:
"There is a systemic problem with staffing. In places like Napier and Dunedin, staff can't get leave. They're cutting costs by keeping on a minimum number of staff.
"When you are tired and you can't get time off, then it becomes dangerous."
Julie-Anne Genter, the Minister in charge of Transport Safety, wouldn't say if she was aware of the issues.
"There is a need to ensure our regulators are taking appropriate action, and so that's something I expect the Ministry of Transport to look closely at."
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Since 2015, there have been 919 incidents relating to air traffic control issues reported to CAA by Airways.
Most were minor, but one in Gisborne in January 2018 could have resulted in death. It involved the pilot of a Robinson 44 who almost hit a drone.
The controller asked the drone to land when the helicopter wanted to return to the airfield, but he failed to tell the chopper pilot.
The air traffic controller thought he saw the drone land, but inquiries found it could actually have been a seagull. The drone was still airborne when the helicopter reported a near miss at 400 feet.
Mr Robinson says a recent staff survey revealed serious issues.
"Airways was reflected as having the bottom 2 percent of all NZ businesses as far as their staff culture went."
Newshub understands industrial tensions are growing, and some staff are talking about taking action.
The CAA told Newshub there are resourcing pressures "from time to time", but that it's satisfied Airways has the ability to carry out effective workforce planning.