The union representing scientists says a potential loss of 83 scientists at AgResearch could mean these experts will leave the country for overseas positions.
AgResearch said it was consulting with staff about a proposal to reduce scientist and technician roles by 20 percent.
The Crown research institute is proposing to cull 33 scientist roles and 50 science technician roles in areas where it said customer demand and the potential for impact was reducing.
New Zealand Association of Scientists president Nicola Gaston said AgResearch's revenue and staffing had been volatile for the last five years.
She said that between 2010 and 2014, AgResearch's revenues fell by 7 percent in real terms, with a dramatic decline in revenue of $5 million in its last reporting period.
Dr Gaston said the redundancies were a major concern.
"Scientists expertise does tend to be quite specific expertise and so there are real questions to be asked about whether some of the expertise will be kept in New Zealand or whether it will go abroad.
"There are some serious questions to be asked, both of the management and governance board of AgResearch about how this has been allowed to happen. It does seem that there's a financial hole which is somehow directly responsible for the current decision in restructuring.
"But again, I think there are questions to be asked about how that has happened, if it's not due to direct funding of science AgResearch by the Government, is it due to inadequacies in the strategy around science funding in New Zealand.
"And does the reliance on the sector to determine where scientists expertise is being supported, does that actually create problems and short-termism in the system," she said.
AgResearch said it would be consulting with staff on what had been proposed and listening to feedback before making any final decisions.