'No clear checks and balances': Australian Antarctic Division reveals $42 million overspend

The revelation comes after the division's operating budget decreased by $25 million this financial year, a drop that has reportedly affected delivery of science projects, put a question mark over contractor jobs and put on hold a number of positions in various recruitment stages.

The government has maintained that the reduction was largely a result of funding for Australia's icebreaking research ship, RSV Nuyina, coming to an end.

But on Thursday, department deputy secretary Sean Sullivan told the inquiry the division also "overspent extraordinarily" by $42 million last year.

"Part of that was because of needing to have two ships, which wasn't ideal, and increased aviation, and it was way beyond what the budget was actually provided for," he said.

"At the same time, when I came into this position, overseeing the Antarctic division ... there were no clear budgets at a branch level.

"There were no clear checks and balances from a governance perspective on interrelationships between projects".

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He said there had also been an "ongoing issue around budget transparency at branch level".

In July, division head Emma Campbell notified staff that the department's operating budget would reduce by $25 million or 16 per cent in the 2023-2024 financial year.

Mr Sullivan said the email was about increasing transparency.

"[That was] to say ... if your expectation is that you think that we're going to have the same amount of budget that you had last year, that's incorrect," he said.

Greens spokesperson for healthy oceans Peter Whish-Wilson said those revelations were "shocking".

"Whether or not the division likes to admit it, this has resulted in budget restraints that have impacted Australia's delivery of critical science programs in the Antarctic," he said.

Senator Peter Whish-Wilson and the opposition's environment spokesman Jonathan Duniam teamed up in August to bring the matter of division funding to an inquiry.

The government has promised the drop in budget would not lead to job losses but flagged that a reduction in spending on contractors and consultants was among the cost saving measures being considered.

Asked about how many contractors could lose their jobs, Ms Campbell said staff were "still working through the budget process".

The inquiry heard the division had 330 ongoing APS staff, 72 non-ongoing APS staff, 94 non-ongoing expedition staff and 53 contractors.

"To imply that all of non-ongoing and contractor staff will lose their jobs is not true," Ms Campbell said.

"We're certainly looking to increase security for ongoing jobs where we can and my recollection is that we've transferred five non-ongoing staff into permanent positions [since June]."

On Wednesday, Tasmanian regional secretary at the Community and Public Sector Union Zac Batchelor told senators the union also understood more than 40 scientific positions at various recruitment stages had been "pulled back".

Ms Campbell told the inquiry that there "was aspiration and expectation in the science branch" about 40 new positions but only 20 of those positions were advertised.

"Four of those have been filled. The rest are on hold pending resolution of the bigger budget picture to see about affordability," she said.

Of those four roles, two positions were filled by individuals on non-ongoing contracts and two were filled as a result of staff promotions.

"One of my responsibilities is making sure we're cautious of recruitment, so that we live within our funding means," Ms Campbell said.

She added that before finalising the budget, she wanted to get staff feedback

"One of the things I've certainly heard since coming in this job is that staff have felt under huge pressure and that their workloads weren't sustainable for a long time," she said.

"Our job as leaders is to help staff identify priorities and to deliver reasonable workloads within their bandwidth."