The Community and Public Sector Union says Agriculture Victoria jobs may be cut, as part of the state government's plans to tackle growing debt.
But CPSU media and communications manager Julian Kennelly said no-one yet knew how many jobs would go, or from which sections.
Mr Kennelly said government departments this week put forward "scenarios" to Treasury on how they could cut costs.
"That could be any combination of cutting consultants, labour hire or not filling vacant positions - but we are currently working 20 per cent staff shortages [across the entire public service], based on vacancies,," Mr Kennelly said.
CPSU federal secretary Karen Batt said the proposed cuts were the biggest to hit the public service since former Liberal premier Ted Baillieu slashed 3600 jobs in 2012.
The union claimed government departments had been told to cut 10 per cent of staff, or the equivalent of up to 6000 jobs.
"The cuts are real - we've had that confirmed at a senior level," Mr Kennelly said.
"The government has said it hasn't made up with its mind as to how many," he said
Departments had been told to find more savings and put recommendations to Treasury.
"So we wait," Mr Kennelly said.
It's just on a year since the government announced the last round of cuts.
The 47 staff were part of a group of 200, who took early retirement across the DJPR.
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"The AgVic jobs were across the board, externally funded roles were less likely to be impacted," Mr Kennelly said.
"Further cuts would put the state in a precarious position to respond to biosecurity emergencies."
These included avian influenza, varroa mite (bees), Khapra beetle (a grain pest) and supporting the agricultural community after the massive impact from rains and floods, including getting feed to stock.
"After the bushfires, AgVic staff spent months providing support to communities and stock feed to livestock owners," he said.
"The reward for same people who responded to bushfires, to floods and the pandemic is that they might not have a job."
In November 2019, 49 soil, pasture and red meat researchers working for Agriculture Victoria were sacked - then reinstated on the same day.
The claims of cuts come as one source said AgVic was planning a major refurbishment of regional offices.
There were plans to modernise the office spaces, the source said, which was seen as a huge waste of money as the premises were more than acceptable.
Mr Kennelly said had not heard about the refurbishment plans,.
"That's going to be an issue, because while there is plenty of money to build things there is no money for people to actually sit in the buildings," he said.
Assistant Treasurer Danny Pearson denied the government had decided to cut jobs.
"We've not made any decision in terms of those issues," he said on Wednesday.
"But we've given the commitment that we're going to honour each of our election commitments and we've given a commitment that we will have a operating surplus at the end of forward estimates."