Researchers warn they cannot wait until the government's Budget at the end of May to find out what is happening with science funding.
Scientists spoken to by RNZ said the uncertainty combined with historic under-funding of the sector would drive away top research talent.
They said the problem was driven by the expiry of the 10-year $680 million national science challenges in a few months combined with the government's scrapping of both its predecessor's reform of the science sector and its $450m spend on science infrastructure in Wellington.
Joanne Todd from the University of Auckland leads the High Value Nutrition challenge which helped companies test the health benefits of their products.
Todd said the lack of a replacement for the challenges was a big problem.
"We've talked about it as our scientists falling off the edge of a cliff. There's very few other options for the food industry in New Zealand to go to for this type of funding so High Value Nutrition has been really unique in that aspect. So it doesn't only leave our scientists without funding, it leaves our industry with not many places to go," she said.
More than 100 scientists worked on the challenge and it had worked with 47 PhD students during its 10-year life span, Todd said.
The science community could not wait until the government's Budget at the end of May to find out what was happening, she said.
"No we can't wait. We're already seeing some of our scientists move on, potentially moving on to more administrative positions or looking into overseas options and it takes a long time to do science in some instances, so if a budget's not in place for a long time then there's a really big hole in this sector," she said.
Jim Mann from Otago University heads the Healthier Lives challenge studying the most serious diseases affecting the New Zealand population.
He told RNZ the challenges were a big success but now New Zealand risked losing researchers while the government decided what to do.
"The big problem now is that we've got a huge gap so yes, there are going to be people who are not going to know where to turn because not only is there nothing in place, but there's not even any news of anything being in place. So come the middle of the year there are going to be people who expected to have jobs that are not going to have jobs," he said.
Professor Mann said the challenges were a new way of funding science, worked well, and scientists had been led to believe there would some form of replacement for them.
"What is particularly sad is that the science challenges have really shown what can be done with this particular funding model and this particular funding model with, at this stage, nothing to take its place," he said.
"It's not the kind of thing where you can just introduce some kind of interim arrangement for a year and carry on... it's too late for that now."
Wayne Cutfield from the University of Auckland leads the Better Start challenge focused on at-risk children.
He said New Zealand's research sector was under-funded compared to other countries and the hiatus was making things worse.
"I think we need signals as soon as possible. This is a really challenging time for researchers to be put into limbo in that in a tight financial environment research funding can be seen as a nice to have, as an extra... in truth research informs our lives, our health, our well-being, our economy, our environment," he said.
"Is there a risk that we could lose scientists? I think the answer is yes and in fact we have lost scientists over the years because of our fragile science funding system and this will simply add to that," he said.
Association of Scientists co-president Troy Baisden said it had become harder to recruit scientists to New Zealand in the past 10 years.
"If we were working in New Zealand ecosystems or natural problems, it was exciting and we had potentially the best in the world. Now, it's difficult to understand to be honest why anyone would want to come place their career in New Zealand research until we fix some of these problems," he said.
New Zealand spent less on science than other countries and the way it spent that money needed an overhaul, he said.
Professor Baisden said the country would miss out on important advances if it did not maintain a strong research base.
"What we're really talking about is losing a future company like Xero, a future thing like Rocket Lab, a future billion-dollar horticultural sector, the possibility of actually having automation and robotics take off for example, maybe in horticulture or wine. All of these things could be on a knife edge," he said.
Minister of Science, Innovation and Technology Judith Collins said she could not comment on what might or might not be in the government's Budget.
"I intend to identify and implement changes that improve the efficiency of the entire science, innovation and technology sector with minimal disruption, while being cognisant of the fact we are operating in an extremely tight fiscal environment," she told RNZ in a statement.