Australian National University Vice-Chancellor Ian Young has described as disappointing a decision by the federal government to replace funding for one axed research program with funding from another.

University of Canberra Vice-Chancellor Stephen Parker said the money should never have been axed in the first place.

Holding true to his word that he would "fix" a $150 million cut to the National Collaborative Research Infrastructure Strategy, Education Minister Christopher Pyne has taken $150 million from the Sustainable Research Excellence Program to fill the hole.

Earlier this year Mr Pyne attempted to bribe the Senate into passing massive deregulation reforms to universities by threatening NCRIS funding. Tuesday's Budget saw the money restored to 27 research facilities across the country.

But the money has come from another valuable sustainable research program - which tops up research block grants - and which will lose $150 million this year, followed by $37.5 million in 2017 and $75 million in 2018 as the Government "adjusts growth" in the program.

Professor Young said "We are relieved that NCRIS has been restored as that is core money for the university, but we are working out the magnitude of the potential impact of the loss of Sustainable Research funding".

"We are disappointed that one research program has come at the cost of another."

Professor Parker noted that the Budget only delivered a one-year extension of funding for NCRIS.

"It should never have been in doubt in the first place".

Professor Young said it was not surprising that higher education played such a minimal role in the Budget given the enormous drama that had played out over recent months with Mr Pyne attempting to push through major reform agenda – and failing twice.

Cooperative Research Centres have also had their funding cut - with the government removing $26.8 million over four years to help "repair the budget".

This year CRCs will take a $1.6 million hit, although the Budget papers stated $732.4 million would continue to flow to the program in line with forward estimates "pending the outcome of a review" which was announced late last year.

Professor Parker said that further federal cuts to education should be voted on by the electorate.

"The Government remains committed to the 20 per cent cut in university funding from 1 January 2016 and to deregulating fully the fees that universities can charge domestic students. The Senate has twice rejected the package already.

"Recent opinion polling suggests that 77 per cent of people believe deregulating universities will mean Australian families have to take on unreasonable debt if they want their children to go to university and 73 per cent believe the federal government should increase the overall amount of funding at universities. If the government wants to persevere it should take the measures to the next election."