Up to 90 jobs are on the line at Niwa, the National Institute of Water and Atmospheric Research, as part of the goverment's directive to pare down the public service.
Public sector bosses have been asked to find proposals to make between 6.5 and 7.5 percent of savings to help the government prune back annual sector spending by $1.5 billion.
On Monday, Ministry for the Environment called for voluntary redundancies, which the Public Service Association said could see hundreds of workers leave. About 30 science and engineering jobs at research organisation Callaghan Innovation could go.
The PSA said Niwa was proposing to cut 85 to 90 roles of which 30 were currently vacant. The cuts amounted to about 13 percent of its workforce.
It said Niwa maintained this would have no impact on its core work.
Are you affected by the public sector cost-cutting measures? Contact kate.green@rnz.co.nz.
PSA assistant secretary Fleur Fitzsimons said the union was "very concerned".
"This wasn't signalled by the government prior to the election, and they do critical research and work about the weather systems, climate change an absolutely fundamental role in our public sector."
New Zealand Association of Scientists co-president Dr Lucy Stewart said expertise will be lost as a result of job cuts in the science sector.
The cuts will also mean Niwa has to halt research in some areas.
"Often we will lose this expertise for the entire nation because we only have one or two people in the country who have some of this expertise and the second thing is that they will go overseas if they can't work here because there aren't really a lot of other jobs ... and then they won't come back."
Stewart said some of the environmental monitoring programmes have already been cut to the point where they are unsustainable.
Niwa has been approached for comment.
Earlier on Tuesday, RNZ reported dozens of jobs were to be axed at Commerce Commission.
RNZ understands 35 to 40 jobs will be cut at the commission, about 10 percent of its staff.