The CSIRO Staff Association expects up to nine energy research jobs will be lost from Newcastle's energy centre as part of a national restructure.
The restructure will result in the loss of 39 jobs from the energy business unit, which has operations around the country.
The CSIRO job losses coincide with anticipated significant job losses at the University of Newcastle.
About 150 staff work at CSIRO Newcastle across several research groups. Seventy of those staff are employed in the energy unit.
Consultation between the staff association and CSIRO concluded recently.
Newcastle staff association representative Mike Collins said the association was working to either stop or mitigate the job losses through redeployment.
The association said the job losses would have a devastating impact on research.
"We keep on talking about the need to have a just energy transition in this country...cutting jobs like these is not the way to achieve it," he said.
He said uncertainty around the government's energy policy meant companies were less willing to invest in commercial partnerships with CSIRO.
"At this time in our history we need as much scientific capacity as possible but the government seems determined to get rid of it."
Community and Public Sector Union (CSIRO section) secretary Sam Popovski said the cuts would have an enduring impact on the national capability to develop energy and climate policy.
"The recent King Review indicates that Australia's energy policy remains far from settled and diminishing CSIRO's specialist capabilities in this area harms government decision-making and future innovation," Mr Popovski said.
"There are growing concerns that the October federal budget may feature spending cuts...the CSIRO Board must ensure that the case for CSIRO public funding is heard loud and clear over coming months.
A CSIRO spokeswoman denied the number of job losses at Newcastle was set.
"We assume the CSIRO Staff Association is picking and choosing a range of numbers associated with movements in our workforce to suggest our staff numbers have changed dramatically. This does not result in their statement being correct," she said.
CSIRO has also denied claims its workforce will be cut by 600.
"As Australia's energy industry shifts away from fossil fuel-based energy dependence, CSIRO is making some changes in its energy business unit, including increasing investment and capability in renewables"
"This is resulting in a reduction of up to 39 roles in areas such as oil, gas and coal, and the creation of up to 12 new roles in areas including hydrogen and digital energy technologies."
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