Staff at CSIRO's world-leading energy research centre at Mayfield fear dozens of jobs will be lost due to cuts resulting from a drop in commercial revenue and an internal restructure.
The centre is part of the CSIRO energy business unit, which also has operations in Melbourne and Perth.
The centre's 250 staff were advised last week that between 42 and 46 jobs would be lost across the unit.
CSIRO employs about 150 staff at Newcastle across several research groups.
About 70 per cent of Newcastle staff are employed by the energy unit.
Staff are yet to be advised how many of the Newcastle-based energy research jobs will be lost.
"This something we have been worried about for some time," CSIRO Newcastle staff association representative Michael Collins said.
"We have seen a continual neglect of science funding over consecutive budgets."
The latest announcement follows on from a 20 per cent cut to staff numbers in 2014, which has resulted in an increased use of contractors.
The federal government is due to unveil its carbon reduction roadmap in coming weeks.
The strategy, which aims to cut carbon emissions to near net zero by 2050, will focus on hydrogen, carbon capture and storage, lithium and livestock feed supplements.
As a result, CSIRO says up to 12 new positions will be created in growth areas.
A CSIRO spokeswoman said the Newcastle Energy Centre would remain a focal point of the organisation's innovative energy research.
"The CSIRO Energy Business Unit is in the process of undertaking capability changes to ensure it is best placed to deliver future energy science and technology solutions. This process includes a proposed reduction in 42-46 roles and the addition of eight to 12 new roles to ensure CSIRO continues to maximise the impact of our key research areas into the future," she said.
"CSIRO has clear and well-established processes for undertaking these changes, including ensuring staff are fully consulted and supported throughout the process consistent with our obligations under the Enterprise Agreement."
Newcastle MP Sharon Claydon said it would be reckless to shed jobs at the energy centre.
"Energy is at the heart of so many national and global challenges. We should be investing in the great work of world-class research institutions like the CSIRO Energy Centre in Newcastle - not laying people off," Ms Claydon said.
"At a time when the government seems incapable of landing a national energy policy it is utterly reckless to risk any further job losses at the CSIRO Energy Centre."
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