The government watchdog also intends to review the Finance Minister's handling of discretionary funds worth almost $43 billion approved in advance by parliament as part of emergency measures.

As the government's focus turns to easing restrictions imposed to slow the spread of the coronavirus, the Australian National Audit Office has outlined its plans to evaluate the effectiveness and efficiency of the Commonwealth's actions.

The office, which unleashed a political firestorm early this year with its revelations about political interference in the administration of the Community Sport Infrastructure Program, has flagged that the $1.1 billion National Medical Stockpile fund and the operations of Services Australia and the Australian Taxation Office are likely to be audited in coming months.

The Health Department has had responsibility for expanding and replenishing the medical stockpile while the ATO has implemented the $130 billion JobKeeper scheme, the early superannuation access program and the business cash flow boost and Services Australia has processed more than a million claims for JobSeeker support.

The speed and scale of the government's emergency response has drawn the Auditor-General's attention.

"Rapid policy design and implementation can present new and increased risks to sound public administration and the proper use of public resources," the audit office said.

It said the proposed audits of Services Australia and the ATO would consider the management of risks arising from the high volume of payments, the potential for fraud and non-compliance, the redeployment of large numbers of public servants and the management of huge amounts of data.

Underlining fraud concerns, the early superannuation access scheme was temporarily suspended late last week following revelations that up to 150 people had had part of their superannuation stolen in an impersonation scam. The government has assured that no ATO or superannuation fund systems were compromised.

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Labor has sharpened its focus on the JobKeeper program, attacking the government for not including casuals who have been with an employer for less than 12 months and criticising the flat $1500 payment which has delivered a huge pay increase to some workers.

Labor's finance spokeswoman Katy Gallagher said "there are issues that can be tightened up with the design of this program. It's an important program. It's currently under-subscribed".

But assistant finance minister Zed Seselja said backed the program's design.

"There is no doubt that when you roll something out as significant as this, and as wide reaching as this, it will not be 100 per cent perfect," Senator Seselja said. "But do we think we've got the settings about, right? Yes."

The audit office plans a separate investigation into the national medical stockpile to "review the procurement of health personal protective equipment, pharmaceuticals and medical devices".

Chief medical officer Brendan Murphy told a Senate committee in April that Australia had paid "premium prices" to secure supplies of face masks in the face of fierce international competition.

"Essentially, the message from government ... has been, 'Spend what you need to make Australia safe'," Professor Murphy told the committee.

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