Labor has described the hit to the independent office as "revenge" for the sports rorts scandal, which claimed the scalp of one minister and revealed the role of a spreadsheet colour-coded by electorate in funding decisions.

In the lead up to the budget, Auditor-General Grant Hehir warned that years of funding cuts to the Australian National Audit Office had taken their toll, and there would be fewer performance audits in future without a cash injection.

Just 42 performance audits were completed in 2019-20, down on the target of 48. Next year that will reduce to 40 audits and by 2023-24 there will be just 38 performance audits, ten fewer than 2018-19.

While funding for assurance audits remains steady, the government is cutting $2.8 million from the allocation for performance audits this year alone, with a further cut of $1.3 million in 2022-23 and $800,000 in 2023-24.

The cut of almost $5 million makes it a certainty that fewer audits of government programs will be completed.

"Without supplementary appropriations, the number of performance audits tabled in the Parliament will continue to reduce," Mr Hehir said in the office's annual report before the budget.

It opens up the possibility that scandals like sports rorts and the $33 million spent on land near the western Sydney airport could go under the radar in future.

"As Australia hurtles towards a trillion dollars of debt and $500 billion in new spending, now is the worst time to be cutting funding to the independent auditor-general," said Labor's Julian Hill, who is deputy chair of the Joint Parliamentary Committee of Accounts and Audit.

"There's no doubt this is revenge for sports rorts and it means Australians are less likely to learn about waste, mistakes in the government's COVID response and new little rorty pots of money which will fall out of this budget for ministers to misuse."

He called on government members of the audit committee, which represents the audit office in parliament, to stand up to the government and defend the audit office against cuts to its funding.

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There are no budget measures for the audit office in the budget and its funding from government for assurance audits will remain stagnant over the forward estimates.

Asked about the funding in question time, Prime Minister Scott Morrison said a ten year review into the Australian National Audit Office was currently underway.

"When the government receives the outcomes of that 10-year review, we will consider the resourcing for the ANAO," he said.

Former counsel assisting at the NSW Independent Commission against Corruption and now director of the Centre for Public Integrity Geoffrey Watson labelled the cuts to the audit office "disgraceful".

"It's transparent that the purpose is to stifle the operations of the investigative authority which has been holding the government to account," he said.

The role of the audit office as an independent watchdog on spending was even more important as the government throws money at stimulus measures, Mr Watson said.

"Concurrently this government has engaged in an unprecedented binge on allowing discretionary spending by non-accountable bodies."

Mr Watson said the audit office had embarrassed the government through its reports on sports rorts and the price paid for land at the Western Sydney Airport, and the cuts were being made while most Australians were distracted by the pandemic.

Labor member for Bean in Canberra's south David Smith said the funding cut was "an act of political bastardry".

"At a time when the government is delivering unprecedented debt and expenditure Australians deserve such spending to be properly scrutinised."

With the introduction of a national integrity commission delayed further, with no more funding for the body, which has been on the backburner since the pandemic.

Instead the Australian Commission for Law Enforcement Integrity will get an extra $700,000 this financial year, but the cost will be met from within the existing budgets of some the agencies it oversees, Australian Criminal Intelligence Commission, the Australian Transaction Reports and Analysis Centre, and parts of the Department of Agriculture, Water and the Environment.

"The government went to the last election promising an independent and properly empowered national integrity commission and last night, contrary to promises made by the Attorney-General the proposed funding for that body was secretly and silently removed," Mr Watson said.