The National Institute of Water and Atmospheric Research (NIWA) is reviewing about 35 positions and has confirmed there are likely to be some redundancies.
Chief executive John Morgan says staff are being consulted and feedback will be considered before any decisions are made.
The institute employs about 730 staff at 15 sites across the country.
The Public Service Association (PSA) says the proposed cuts include 17 science positions, most of which will be from Wellington's regional office.
The union describes the move as short-sighted, saying it could set back innovation and economic gains in the environmental sector.
PSA national secretary Richard Wagstaff says Government spending cuts across the board have led to the proposed cuts.
The New Zealand Association of Scientists says there's a high level of anxiety among scientists working for Crown Research Institutes.
Vice-president, Shaun Hendy says there's a long-term trend of flat government funding for Crown research .
Shaun Hendy says all scientists working for a Crown Research Institute would be feeling unsure about their working future.