Federal Court Justice Richard White has reserved his decision after an all-day hearing on Wednesday on whether the pandemic deliberations of the national cabinet should be made public.

The prime minister's lawyers are resisting independent senator Rex Patrick's demand for Australians to see the shared medical advice driving decisions on borders, lockdowns, vaccinations, school closures, the aged care death toll and failures in disability.

Andrew Berger QC told the Administrative Appeals Tribunal it was irrelevant that there'd never been a national cabinet before Scott Morrison set it up last year.

"The national cabinet is a committee of cabinet because it operates like one," he said.

Cloaking discussions in confidentiality under cabinet practices allowed candid discussions in these "exceptional times", he said.

In contrast, the now defunct Council of Australian Governments process stifled reform.

Mr Berger argued the paper trail to and from the committee of Australia's prime minister, premiers and chief ministers must be exempt from freedom of information laws.

Five hours into proceedings, Justice White asked for primary evidence about a decision being made to set up the national cabinet, rather than hundreds of pages of material from which various inferences could be made.

Mr Berger referred him to a sealed envelope containing a note attached to a cabinet minute from March 15, 2020.

Justice White also issued an order that he see the terms of reference for the national cabinet.

He had asked how it could be determined the document was relevant if he couldn't read it, prompting its swift delivery to the courtroom for his eyes only.

The crucial document remains off-limits for ordinary Australians, and Senator Patrick, for now.

Justice White suggested the terms of reference were "in a different category" from advice and records of discussions of leaders on various topics.

But Mr Berger warned showing "the very first card in the deck" could be seen as an intrusion into confidentiality.

"The national cabinet has achieved a lot of positive outcomes and that has served the public," he said.

The prime minister has long argued that national cabinet discussions, including medical advice on borders and vaccinations, must be kept secret.

Any paperwork marked "cabinet-in-confidence" is cloaked in tight secrecy, which currently shrouds all advice to the national cabinet, the emergency Australian Health Protection Principal Committee of top health officers, and the National COVID-19 Coordination Commission of business leaders.

Senator Patrick says it is arrogant of the prime minister to be "unilaterally and unlawfully wrapping a secrecy blanket" around decisions.

"That thing we know as a cabinet is not changeable just because of the desire of the prime minister of the day," said Geoffrey Watson SC, for Senator Patrick.

Mr Watson also rejected the "expert" statements from prime minister's department Secretary Phil Gaetjens and First Assistant Secretary Leonie McGregor, saying it was opinion verging on "Dorothy Dixer".

No date was set for the next hearing.

Australian Associated Press