Independent ACT senator David Pocock said the warning bells followed a decade of funding cuts to the Australian National Audit Office, which have already resulted in nearly a quarter of audits being dropped.

The independent body is expected to deliver 42 performance audits during the 2022-23 financial year but warned a combination of factors were placing that target "at risk".

Auditor-General Grant Hehir and his team are already at work on a selection of audits, including an examination of the millions spent on office furniture at Services Australia and the Home Affairs Department along with assessing whether the Department of Defence's assistance to Ukraine has been effective.

But the creation of two new departments - the Climate Change and Workplace Relations departments - in July by Prime Minister Anthony Albanese has put a spanner in the works for its future investigations.

The watchdog now needs to undertake audits of the two department's financial statements in addition to its other work without increased funding and resourcing, it said in a recently-answered question on notice.

It means staff will need to be redirected from other projects to undertake the additional work, placing pressure on its ability to deliver the 42 audits.

ANAO received an $8 million boost in the Albanese government's October federal budget with its staffing level also being bumped up by 53 to 379.

But the cash injection hasn't improved the situation with the training of new auditors and a series of unexpected absences, particularly at the audit manager level, further delaying work.

The watchdog said no specific audits were on the cutting room floor as of yet but a final list would be determined by the priorities of Parliament, community interest and opportunities Mr Hehir sees to demonstrate good practice in public administration and accountability.

Senator Pocock said it was critical the federal government give the office enough resources to ensure integrity across government processes.

"Over the past decade the ANAO has had its budget cut so frequently, and by so much, that the target number of audits it can complete has fallen from 55 in 2011-12 to just 42 this financial year," he said.

"Now we learn that even that significantly reduced number of audits may not be conducted because its functions have been expanded without expanding its resourcing, leading to significant staffing challenges."

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Funding for the ANAO has been in the spotlight in recent years after it was peeled back following a string of explosive reports relating to mismanagement under the former Coalition government.

Scandals, such as sports rorts and the $33 million spent on overvalued land near the western Sydney airport, were revealed as part of the independent office's work.

Senator Pocock said these revelations are exactly why the audit office needed adequate and consistent funding to do the task.

"While most Australians haven't heard of the ANAO, it plays a key role in supporting good governance and shining a light on poor use of taxpayer money," he said.

"It needs long-term funding certainty that adequately resources it to do the vital job it is meant to do.

"It's clear the community expects and deserves strong, properly resourced oversight of how taxpayer money is spent. That's the job of the ANAO and that's why it's so important we get its resourcing right."