Up to 1500 jobs are under review at the CSIRO, as Australia's premier scientific research organisation looks to shed staff to meet its public service staffing cap, its union says.
But the agency has rejected the figure as "incorrect and pure speculation".
The CSIRO Staff Association says 40 casual and fixed-term jobs have not been renewed since the average staffing level cap began to bite in July.
It has stepped up its campaign to insulate the agency from further job losses, writing to politicians in the past week to call for the cap to be scrapped.
CSIRO Staff Association secretary Sam Popovski estimates between 170 and 200 positions will be lost due to the restriction.
"The CSIRO has about 5500 staff so it's a fair chunk across the board," Mr Popovski said.
He said the main way the agency had been trying to meet the cap was to review the term contract or casual positions to determine which ones would not be renewed.
"It's more cost-effective than redundancies," Mr Popovski said.
"It's really unfortunate because term contract staff are disproportionately younger mid-career scientists and engineers, women and Aboriginal and Torres Strait Islander people.
"We're concerned we'll lose people to the science industry in their late 20s and early 30s if they continue to be targeted. There's not many science jobs in the university and private sector, in Australia R&D only accounts for 1.8 per cent of gross domestic product, which is much lower than the OECD average."
Mr Popovski is also concerned the cuts will be a further drain on the Australian economy.
The CSIRO generated $433 million of revenue from research, consultancy and testing services in 2018-19.
But even jobs that were fully funded by industry had been lost, Mr Popovski said.
"Already we know of several people who haven't had their contract renewed, even though all of their job is paid for by industry, and not by the taxpayer," he said.
He has "conservatively estimated" the cap would cost CSIRO about $15 million in lost revenue from the private sector, and a consequent $180 million to GDP.
"The innovation economy and science sector is relatively small and specialised in this country, people know who they want to work with. We've seen industry, once certain staff have been removed, say they'll no longer fund the CSIRO for future work," Mr Popovski said.
At the very least, the cap on industry-funded positions should be removed, Mr Popovski argued.
But CSIRO spokesman Huw Morgan dismissed the union's concerns.
"Claims made that '1500 fixed term and casual positions are under review right now in order to meet the cap', or that 'the job reduction needed to meet the cap - at least 170 - could cost the CSIRO $15 million in lost revenue' are pure speculation and incorrect," Mr Morgan said.
"The average staffing level is applied at the portfolio level and assigned to each agency. Within CSIRO, each area, whether that be a science or support area, is able to carefully consider how it will manage resourcing from both a budget and [average staffing level] perspective, while continuing to deliver excellent science and scientific advice for the benefit of Australia, as it has done for over 100 years. [Average staffing level] has been in place since 2013, and CSIRO, like other government agencies, is required to manage to its estimate."
Finance Minister Mathias Cormann would also not be drawn on whether the cap could be relaxed for jobs paid for by industry.
"The government continues to promote a flexible approach to resourcing that strikes the right balance between a talented core workforce of permanent public servants and selective use of external expertise," Senator Cormann said.
It comes after the staff association wrote last month to a parliamentary inquiry, urging politicians to force CSIRO executives to provide evidence about the extent of the use of external contractors, consultants and labour hire staff.
The association said young scientists were being encouraged to set up ABNs, so they could be hired as external contractors.