Federal agriculture officials did not speak to the doctor on board the Ruby Princess cruise ship before passengers disembarked in Sydney.
Department of Agriculture, Water and the Environment secretary Andrew Metcalfe admitted to a Senate inquiry on Tuesday that protocols weren't followed on the ship.
The vessel has been linked to 28 coronavirus deaths and hundreds of cases, with a NSW inquiry into its Sydney disembarkment laying most of the blame on state health authorities.
But Mr Metcalfe says the process for completing a traveller illness checklist was not followed by federal agriculture officials.
"I now understand that the local application of the protocols at the Port of Sydney, in relation to cruise ships, was for my officers not to administer TICs but to consult with medical officers on the ships to get notified of any health issues," he said.
"I am advised that on this particular occasion our officer only relied on the NSW medical assessment."
NSW Health had deemed the ship "low risk".
Mr Metcalfe stressed his department's main focus was on plant and animal biosecurity risks but said it had a role in the human biosecurity framework.
It remains unclear who gave oral advice for passengers to disembark about 6.30am on March 19, about an hour before Agriculture spoke to NSW Health.
Labor senator Kristina Keneally suggested the approval may have occurred through omission, after Mr Metcalfe said his two officers didn't prevent people from getting off the ship.
Australian Border Force was absolved of any part in the debacle through the NSW inquiry.
ABF granted approval for people to leave the ship under customs and immigration law, but not health.
An ABF officer misinterpreted negative flu tests for negative coronavirus tests, but that played no role in passengers leaving the ship.
ABF commissioner Michael Outram admitted the officer wasn't operating under law by being involved with health tests, but was trying to be helpful.
NSW Premier Gladys Berejiklian has apologised over the saga and promised to implement all recommendations from the inquiry.
In Victoria, 222 new virus infections were recorded on Tuesday, its lowest number of daily detections in a month. The state recorded another 17 deaths in the previous 24 hours, taking the national toll to 438.
"We continue to see a decline in daily figures, which is very encouraging and a huge credit to the people of the state," deputy chief medical officer Michael Kidd told reporters in Canberra.
But he said Victorians should continue to get tested and stick to the restrictions.
An inquiry into Victoria's hotel quarantine program has heard almost all the state's second wave of cases can be traced back to overseas travellers at two hotels.
NSW has recorded only three new virus cases in the 24 hours to 8pm on Monday, the lowest number in more than a month.
Queensland warns its borders could remain sealed for several months or until its coronavirus infections have fallen to zero.
Western Australia has cancelled its annual royal show and postponed phase five restrictions for another two months in a bid to prevent the spread of COVID-19.
Tasmania's borders will remain closed until at least December 1.
Australian Associated Press