The threatened jobs come on top of scores of university science positions on the chopping block if the Australian Renewable Energy Agency is de-funded as part of the government's ``budget repair" omnibus bill currently before the Parliament.

The new threat to CSIRO research comes less than a month after Science Minister Greg Hunt instructed the organisation to renew its focus on climate science, claiming it would be a "bedrock function" of the agency's activities.

Fairfax reported on Wednesday that Australia's leading renewables researchers were warning the nation was heading towards the "clean energy valley of death" if the ARENA cuts are passed.

Privately funded energy projects have already been thrown into doubt by the uncertainty surrounding ARENA's future, it was reported on Wednesday, and industry lobbyists predict that worse is to come.

ARENA was established in 2012 by the Gillard government to fund research into renewable energy, and was abolished by the Abbott government in 2014.

The agency received a stay of execution in March 2016 but Coalition policy now wants to strip $1.3 billion of funding from ARENA and merge its funding role with the Clean Energy Finance Corporation, which expects to see a financial return on money it invests in research.

But opposition to the cuts is growing with Greens Leader Richard Di Natale urging Labor to oppose the Coalition's plan.

Many Labor MPs are understood to be unhappy about the proposed cuts, and the party's environment spokesman, Tony Burke, has complained it is not the same plan the opposition agreed to before the election.

But Labor has yet to publicly declare its position on ARENA and Energy Minister Josh Frydenberg has not responded to a request for comment on the threat to the agency's funding.

The jobs of dozens of researchers at both the Australian National University and the University of NSW, and many more around the nation, will be in doubt if the cuts go ahead, but a substantial number of positions at the CSIRO are also set to go if ARENA is de-funded.

The organisation's main workplace union, the CPSU, says that ordinary Australians would suffer if the CSIRO's clean energy research was curtailed.

"CSIRO is heavily involved in cutting-edge energy research that will benefit ordinary Australians now and into the future, including the National Solar Energy Centre in Newcastle and the Australian Solar Thermal Research Initiative," the union's Assistant National Secretary, Michael Tull, said.

"Slashing ARENA is a short-sighted decision that will have terrible flow-on impacts.

"CSIRO and ARENA are essential to creating renewable energy jobs and making energy more affordable for all Australians.

"ARENA funding accounts for more than 40 per cent of CSIRO's energy research, and more than 120 scientists' jobs will be at risk if ARENA is cut."