Doctors say new software being rolled out nationwide will make it harder to decide on a pilot's fitness to fly.
They are telling the Civil Aviation Authority (CAA) to backpedal on a multimillion-dollar German IT system they say has already failed across the Tasman.
They are also asking why the CAA has not taken up Australia's offer to share its system for free, or evaluated New Zealand software that many examiners - including those at Air New Zealand - already use.
Fifty trained doctors perform 5000-6000 checks on pilots and air traffic controllers every year.
The system, which records and tracks the history of each person before sharing the results, is designed to help keep air travellers safer.
CAA paid about $4m for a German system - EMPIC - three years ago. It was designed to handle many IT tasks, including medical assessments, and the CAA wants everyone to be using it by mid-year.
The Aviation Medical Society (AMSANZ), wrote to Civil Aviation yesterday, pleading with it to hold off on the IT system.
"In its planned form, it does not deliver a safe, efficient and [internationally] compliant aeromedical system," wrote president Dr Michael Drane in an open letter.
He called it "out of date" and "cumbersome", with "extremely limited medical classification and data-mining capability".
It said it presented "a risk to the integrity of the aeromedical regulatory system".
Queenstown doctor Ben Johnston said examiners would be left with a tool that did not do what they needed.
"It's going to be very difficult for medical examiners to necessarily have access to all the information they need, and that situational awareness is really, really important when you're making a decision about a person's fitness to fly," Dr Johnston told RNZ.
'The feedback was pretty negative'
AMSANZ told the CAA in December that EMPIC was "poorly suited to the risk-based approach to regulatory medicine practised in Australasia".
It is widely used in Europe which has a much more rules-based, black-and-white system.
Dr Greg van der Hulst - who helped write the letter to the CAA - said two years ago doctors gave the agency the message that this might not work.
"The feedback was pretty negative. Then everything went quiet and the next we hear at the end of 2023 was, 'here's a working group to how we're going to implement the software'."
The doctors said Australia was forced to salvage EMPIC's medical module years ago by creating new software - MRS.
It had since offered this software to this country for free, the society's letter said.
But the authority did not appear to have looked into that, nor evaluated the existing Skycert medical check system already in use, Dr van der Hulst said.
"We've written... to ask him [the director] to take our concerns seriously and to give us some pause, before we pour more money into a system that may not deliver."
He added that the CAA had people who knew about these issues, but that it appeared its IT team had not talked to them.
And it became clear for the first time a fortnight ago that officials were forging ahead.
Dr Peter Hurly of Palmerston North also felt left in the dark.
He said he had used, and liked, both alternative systems - MRS and Skycert - but he knew far too little about EMPIC, and nothing about the meetings with examiners that CAA began having about it back in December.
"I'm not confident about it until I actually know what it's going to involve, and I do think it's probably a bit draconian the way it seems to be forced on us."
He said it might be enough to make him quit the work.
"If it really becomes too difficult to use and too time consuming, then I might say, 'Well, what's the point?'."
The number of aviation medical examiners has been slowly dwindling, and now sits at about 50.
There are just two in the central region. A pilot at Kapiti aero club said they had to book months in advance in order to get an appointment.
Dr Johnston said the CAA should have asked pilots and air traffic controllers and examiners what they needed first.
RNZ approached EMPIC for comment, which said CAA would handle the request.
CAA defends 'platform for the future'
The Civil Aviation Authority said it would not compromise safety in issuing medical certificates for pilots, as it upgraded its IT system.
The transition needs to be completed by the end of 2024, and within the $16m budget.
CAA deputy chief executive Mike Hill told Morning Report a decision was made to replace old software by purchasing a commercial off-the-shelf product, instead of developing and investing heavily in one in-house.
The medical module was one part of the new software.
Hill said CAA met with a range of doctors from December through to February, asking for feedback.
"This software is used by around 40 other regulators around the world in the same international environment. We all have to comply with the international rules. What we are tackling with is how much of the software do we use.
"We don't want to have anything less than today, which is simply processing.
"The doctors must have access to the previous history to make valid decisions on behalf of the director of the Civil Aviation Authority."
Compared with Australia, he said New Zealand had a less centralised approach with important decisions being made by certified medical examiners. "So of course we're listening to them and their concerns."
He said the software could be amended to fit the country's needs.
Australia looked at the software 10 years ago, before opting out, Hill said.
"Australia has invested heavily in their software.
"What we're also looking for is an end-to-end regulatory process, rather than individual bespoke applications for medical or for licensing or for certification."
He said the end-to-end processing would help avoid duplication and the risk of errors.
Skycert is an NZ company which was used by about 50 percent of doctors for processing, Hill said.
"We're not preventing anyone from using Skycert at this point in time, because Skycert is doing a different set of applications or decision-making or processing than what we need to do.
"We need the entry, we need the gatekeeping, and the processing. How the doctors access the important medical history, we're looking at all of those options at this point in time."
It was a matter of balancing scope, time and cost.
"We have $16m to get off our old software. Once we get off that software, it's the platform for the future to improve."