GNS Science has confirmed dozens of jobs are likely to go at the Crown Research Institute.
It says it is obligated to be financially sustainable and it is facing the same economic challenges as the rest of the country.
Have you been affected by public sector job cuts? Share your story at: hamish.cardwell@rnz.co.nz.
The organisation's change proposal, leaked to RNZ, says 66 roles would likely go from the workforce of 528 people.
About a third of the roles are already vacant, with both science and back office jobs likely to go.
GNS says it is supporting its staff through the unsettling and uncertain time, but it will continue to deliver the critical science, innovation, and technology.
"Growing our financial sustainability is critical if we are to make strategic investments - in our people, and in the assets, technologies, and capabilities required to deliver our critical science and science services now, and for years to come," GNS Science chief exectutive Chelydra Percy said.
"We have been focused on operating with fiscal prudence, seeking cost savings where possible and looking hard at any discretionary spending. Now, considering the size of our workforce alongside other cost saving measures is a difficult but necessary step on a longer journey to financial sustainability."
It wants staff input on the proposal.
'They're being very cavalier with people's lives'
A GNS Science employee, who RNZ has agreed not to name, said the cuts were "drastic" and staff were furious.
Staff understood budget was a problem, but they did not buy that "sweeping reorganisation" was necessary, he said.
"It seems to me that they're being very cavalier with people's lives here, and that's just not right."
The proposed cuts were distributed across the organisation, and included researchers and technicians.
"That's going to have an immediate and profound effect on the volume of research, the quality of research, the quality of work that we can do ... I consider our work to be very important because we deal with earthquakes, volcano monitoring, you know, people's lives are in play," he said.
Staff were upset and there was a lot of resistance to the proposals, he said.
An all-staff meeting with chief executive Chelydra Percy was set to be held on Wednesday afternoon, and the employee expected there would be "a great deal of confrontation".
Union claims cuts at GNS takes science jobs axed to 400
The Public Service Association said the cuts would undermine the organisation's critical work helping New Zealand adapt to climate change and manage risks from earthquakes, tsunami and volcanic eruptions.
And they were contrary to information given to staff via an internal memo in March, it said.
"The proposed cuts make little sense when GNS was profitable only a few months ago," assistant secretary Fleur Fitzsimons said.
"On 1 March the chief executive told staff: 'Our financial results - yet to be audited - are positive. We are up on revenue and sitting at a profit. Overall, we're in a much better position than we were at this time last year'."
But GNS said "long term financial sustainability" was its primary reason for change.
Fitzsimons said if the changes went ahead, they would take the total number of roles lost in the science and research sector to more than 400, as detailed in the Save Science Coalition report.
"This is a sad day for science in Aotearoa and just more proof of the low value this government places on science and research."
The cuts - like those at Callaghan Innovation, NIWA and elsewhere - were happening in the absence of a science strategy from the government which is being prepared by Sir Peter Gluckman's Science System Advisory Group, she said.
"How can the Science System Advisory Group plot a path forward when the system is being devastated in this way?"
GNS Science shareholding ministers - Science Minister Judith Collins and Finance Minister Nicola Willis - declined to comment.