AgResearch staff in Dunedin and elsewhere in the country were feeling "anxiety and uncertainty" after the Crown Research Institute announced it was seeking voluntary severances, PSA national secretary Richard Wagstaff said.
AgResearch employs 150 scientists and other support staff in Dunedin, 140 of them at the Invermay Agricultural Centre and the others at the AgResearch Molecular Biology Unit.
The unit involves a partnership with the University of Otago and is based on campus.
AgResearch chief executive Dr Andy West said staff reductions totalling $2.4 million per year were sought throughout the country.
It was not clear at this stage exactly how many staff that would involve, either nationally or in Dunedin, Dr West said.
He emphasised AgResearch was strongly committed to a new Centre for Reproduction and Genomics, involving about 50 staff in a joint AgResearch-Otago University team.
The centre will be housed in a $17 million complex being built at Invermay.
Nine AgResearch staff at the centre have relocated south from Wallaceville, near Wellington.
Mr Wagstaff said staff cuts could be as high as 40 throughout the country, although the final picture was still unclear.
Dr West said AgResearch was "downsizing" its scientific staff throughout the country and would subsequently also review corporate staffing to ensure the CRI remained sufficiently profitable.
The CRI intended to save about $5 million in costs this financial year, having already cut corporate operational spending by more than $2 million, Dr West said.
The need to tighten the CRI's operations had arisen from a recent combination of several forces: including a significant downturn in two of its most important client industries (sheep and beef).
The institute's long-term commitment to employing under-funded scientists and maintaining unfunded flocks and herds of rare animal genetics also now exceeded its capacity to do so, he said.
AgResearch had opened voluntary severance applications late last week.
These would close on October 22, with results announced on October 31, AgResearch officials said.
Mr Wagstaff said New Zealand could not afford to cut the jobs of scientists whose research helped generate more than $10 billion of exports a year through the country's pastoral farming industry.
PSA has 500 members working at AgResearch throughout the country.
Scientists trained for "a very specialised career" which was not particularly well paid in New Zealand.
Instead of gaining stability, scientists now found some of their jobs were at risk, Mr Wagstaff said.
"It's just not a fair go,"he said.
Dr Peter Dearden, who chairs the Ozone group of leading young Otago University scientists, said laying off AgResearch scientists was not in the country's best interests.
"It sends the message that training to be a scientist in New Zealand may be foolish because there are no jobs," Dr Dearden said.
AgResearch scientists were supporting the country's primary industry.
"If there's anything our science should be doing, it should be doing that," he said.