Federal government agencies undertook the pandemic-planning scenario at the request of Home Affairs department secretary Mike Pezzullo in early 2018 but the results, including the issues it uncovered, never reached the minister's office until one month after Australia entered lockdown, an audit report has found.

The Australian National Audit Office said its probe revealed an annotation on a draft ministerial submission intended for Mr Dutton suggested it hadn't been sent because the results highlighted "significant concerns not being, or not able to be, addressed".

The results of the stress test were later sent to Mr Dutton's office in April 2020, months after the first COVID case was detected. The audit office said it had outlined key findings and actions that had since been undertaken to address them.

The stress test was based on a scenario where a pandemic-scale outbreak commencing in China had occurred and escalated in severity over a nine-month period.

It was designed to help define Home Affairs' role in such a scenario.

It concluded Australia's systems and arrangements would "sufficiently manage and mitigate the impact of ordinary crises, however, a very significant or near-existential crisis would push current arrangements beyond their limits".

The report also noted "Australia's reliance on trade means that the economic and social costs of closing the border during an influenza pandemic would most likely outweigh its benefits".

Mr Pezzullo was not provided a copy of the draft ministerial submission of the results either, the audit report said.

In February 2020, the Home Affairs head informed Prime Minister Scott Morrison, Mr Dutton and then-cabinet secretary Andrew Shearer that the country's whole-of-government civil contingency planning was "outdated and not fit for purpose".

The audit office found Mr Pezzullo's department, in conjunction with the Health Department, began planning for "an extreme national catastrophic pandemic disaster".

However, the plan did not include travel restrictions or mass quarantine arrivals in line with an earlier review finding conducted by Health that found border controls were not effective in stopping a contagious pandemic from reaching Australia.

When the pandemic restrictions came into effect in March, Home Affairs had less than 24 hours to implement the exemption plan.

It was also highlighted in the report that state and territory governments raised ongoing concerns about national coordination and the federal government not adequately sharing information.

The report reads "insufficient information" was provided to state and territory entities running facilities and "there was a lack of national co-ordination for issues relating to mandatory quarantine".

Home Affairs did not properly comply with inbound and outbound visa exemptions while Australia's borders were sealed shut from the outside world during the pandemic, the report found.

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It did not consistently comply with travel exemptions for people needing to come and go from the country during the pandemic.

Australia's travel restriction regime was effective to reduce the risks from the virus, the report found, noting health advice initially informed policy and procedures around limiting travel flows.

Home Affairs also did not update adequate information to airlines about changing travel restrictions to Australia, with one airline stating the approach was a "source of concern and confusion".

The ANAO report found inconsistencies in the approval of travel exemptions, which did not follow protocol guidelines.

"Policies and procedures have not been consistently complied with," the report said.

"Decisions about inward travel exemptions have not consistently been managed in accordance with policies and procedures.

"There were also cases where inconsistent decisions were made even where there was conformance with policy."

It placed greater emphasis on outward exemption timeliness deteriorating during 2021.

"Decisions about outward travel exemptions have not consistently complied with policies and procedures, and there are indications that decision-making has not always been consistent even when in conformance with policy," the report said.

The report noted inbound-travel visas had improved in terms of timeliness.

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