Scientists are challenging their minister's claim there are not serious problems with the $133.5 million National Science Challenges programme.
The aim of the challenges is to find innovative solutions to some of the most fundamental issues facing the country.
Radio New Zealand on Monday reported detailed criticisms scientists had emailed to the Government about the project. The complaints included claims the challenges were too broad, too rigid and would not produce high-quality research.
Science and Innovation Minister Steven Joyce said the project was proceeding well and had no systemic problems.
But New Zealand Association of Scientists President Dr Nicola Gaston said the problems were widespread and scientists felt disillusioned and frustrated.
"At some point you've got to think about the opportunity cost of just putting the money somewhere else. If it were my decision, yes, I'd probably just put it into the Marsden Fund."