The research community has criticised the government's decision to cut university research funding to pay for research facilities, saying it's like removing an engine from a jumbo jet.

Tuesday's budget handed $150 million dollars to the National Collaborative Research Infrastructure Strategy so 27 world-class research facilities could operate for another year.

But the reprieve for NCRIS - which funds radio telescopes used for high-precision GPS, high-end microscopes, cleanrooms to develop new materials, and Australia's ocean surveillance system - comes at a hefty cost for universities. Their research funding will be cut by $300 million over the next four years. They say less research will be done in Australia as a result.

The sustainable research excellence scheme pays for the additional costs of carrying out research at universities, such as laboratories, computers, buildings, technical and professional staff and junior researchers.

The head of the Australian Academy of Science Andrew Holmes said: "Cutting block grants to researchers in universities is like taking engines off the jumbo jet."

"You need to fund the scientists as well as the tools they need to do their work, it can't be one or the other. NCRIS needs a long-term sustainable funding model," said Professor Holmes.

The Academy's science policy secretary Les Field said universities would have to absorb these indirect costs of research, with the larger universities likely to be most affected.

Professor Field, who is also the deputy vice-chancellor of research at the University of NSW, estimated large universities would lose about $10 million each a year because they were given more money through the scheme, commensurate with the amount of research they conducted.

"It'll mean less research is done at the universities as a result," he said.

Universities Australia chief executive Belinda Robinson said the cuts were a "severe blow" to the sector and came on top of previous cuts to research block grants over the past three years, including $500 million stripped from the SRE program over four years from 2012.

"These cuts not only negatively affect universities with established research profiles but also those who depend on this funding to continue to build their research capability," said Ms Robinson.

"Against the backdrop of low commodity prices and the downturn in traditional industries, a prudent approach to stimulating economic renewal is to invest in, not cut, wealth-generating activities like higher education, research and innovation," said Ms Robinson.

Scientists campaigned for months earlier this year to have the government split funding for NCRIS from its controversial higher education reforms, which have stalled in the Senate.

In March education minister Christopher Pyne backed down and released the $150 million to keep the facilities open for 2015-2016, saving about 1700 jobs. Last night's budget set aside money for the following year.

More than 35,000 Australian and international researchers use the facilities, not all of whom work at universities.

"Speaking as a DVC of one of the universities, we don't use all of the facilities," said Professor Field.

"If you'd told me this was the way it was going to happen, I would have been more selective and said my university only uses some of the facilities I'd be happy to support those," he said.

"But that undermines the whole purpose of NCRIS in being a national facility."

Chief scientist Ian Chubb and businessman Philip Clark are leading a review of how to fund research infrastructure over the long term, due mid this year.