Secretary Mike Pezzullo said he and minister Peter Dutton were aware of stress tests being conducted by the department into how it would handle "catastrophic crises", but admitted neither had seen a prepared ministerial submission on the matter.

The Australian National Audit Office revealed a submission on the stress testing had been written but was not passed on up that chain.

The ANAO report said if border closure due to pandemic lasting for nine months was to occur, the Department of Home Affairs would not be able to cope.

Labor senator Kristina Keneally said the ANAO noted "the deputy secretary wrote on the submission that it would 'highlight significant concerns not being or able to be addressed'".

Mr Pezzullo said the judgement of his deputies "had failed them ... on this occasion".

"The question for contingency planning for catastrophic of near existential crises, of which a pandemic stress was one we did look at in early 2018, I have a recollection that it was certainly in Mr Dutton's mind we had done it," he told Senate estimates.

"The ANAO report shows we clearly didn't follow through (providing it as a submission), to my displeasure. I can assure you it won't happen again."

He said while the written advice should have been provided to the minister, the government was well aware the stress testing was being conducted and the minister had other briefing methods available to him.

But Mr Pezzullo added that despite the submission not making it to his or his minister's desk, the department had all contingency planning in place to handle the pandemic.

"I assured Mr Dutton - and history bore this out - that were an existential or catastrophic crisis to confront the nation, we would have the emergency management and national coordination arrangements in place that were fit for purpose," he said.

"We did our job on the substance, we didn't do our job on the paperwork."

Senator Keneally then chastised the secretary for failures in the system that lead to the Ruby Princess outbreak, 40,000 Australians stranded overseas, including hundreds of unaccompanied children, the Delta outbreak stemming from the quarantine transport system and no digital passenger cards that resulted in the Novak Djokovic visa saga.

"Are you seriously contending that we haven't experienced significant stresses that this stress test in fact predicted would happen?" she said.

Mr Pezzullo retorted: "No, what I am contending is that everything my department needed to put in place to be prepared for the eventualities you described, we did."

"We were more than ready for the pandemic that subsequently emerged some two years later."

Australian Associated Press