Anthony Scott, executive director of the Association of Crown Research Institutes, said he understood that "a large number" of the nine crown institutes had suffered a net funding loss in this year's allocations by the Foundation for Research, Science and Technology.
Funding has been switched to universities and private sector companies.
The president of the Institute of Agricultural Scientists, Dr Jacqueline Rowarth, said people within HortResearch had told her that their institute's funding had been cut variously by $5 million, $6.5 million and $8 million.
"I don't know how they can survive that," she said.
"One calculation is that 60 to 80 people in HortResearch are affected. The foundation will say there will be more jobs for scientists elsewhere. But you can't turn a soil scientist into a gene jockey."
The foundation said on Friday that it had allocated $110 million in the new funding round, which takes effect on July 1.
This is about a third of its budget, and represents the first year of a three-year review of Government research contracts.
The foundation's portfolio manager, Dr John Smart, said "transition arrangements" would be negotiated with affected researchers.
These may involve spreading the cuts over several years.
Dr Warrington said he could not say what effect the cuts would have on science providers such as HortResearch until these negotiations were completed.
He said the HortResearch board met on Friday and reaffirmed the institute's business plan, which aims to win more research contracts from local and overseas companies to make up for lower state funding.
In the current financial year to date, the institute's total revenue is up $2.6 million, despite a $500,000 drop in Crown funding.
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