The Ruby Princess cruise ship was assessed as "low risk" for coronavirus infections based on an outdated log of ill passengers on board, an inquiry has heard.

The Carnival vessel became the largest single source of COVID-19 cases in Australia after its 2,700 passengers disembarked at Sydney's Circular Quay on March 19.

It has so far been linked to more than 660 cases and 21 deaths.

A special commission of inquiry into the ill-fated voyage today heard under guidelines implemented the same day the ship docked, NSW Health had to be informed if there had been a respiratory outbreak of more than 1 per cent of passengers on board.

Counsel Assisting the Inquiry, Richard Beasley SC, said a NSW Health team assessed the vessel as "low risk" by at least 4.40pm on the day before the ship arrived, but possibly earlier.

The ship's log used to make that assessment recorded 36 of the 3,795 people on board had presented to the medical centre with relevant symptoms — 0.94 per cent.

As the 1 per cent threshold had not been reached, passengers were allowed to disembark at Circular Quay the next day without any teams from NSW Health boarding to ship to make assessments.

"[But] by 19 March when the ship docked, the 1 per cent level had been reached, although that data was not before the health assessment panel when their determination was made," Mr Beasley said.

The inquiry also heard a request for medical transfer of two ill passengers caused "concern and confusion", especially within NSW Ambulance, over what precautions paramedics should take.

At one point the ship's booking for an ambulance was cancelled but then reinstated because there was concern a passenger had already been diagnosed with coronavirus.

Mr Beasley said tracking the phone calls between NSW Ambulance, NSW Ports, Carnival and officers claiming to be from Australian Border Force and Home Affairs was difficult.

"That confusion is such that even listening to tapes of the calls where they exist does not make what happened easy to follow," he said.

Last month, a senior doctor on board the ship told the inquiry she would not have let passengers disembark when they did.

"I was surprised that we were allowed to do that without waiting for the results to come through," Ilse Von Watzdorf said.

"If it was my decision I would've perhaps waited like the previous time."

NSW Premier Gladys Berejiklian has admitted a "horrible series of mistakes" led to the passengers being given the green-light to disembark.

The inquiry is due to report by mid-August.

NSW Police are conducting a separate, criminal investigation into the circumstances surrounding the Ruby Princess's arrival in Sydney.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume.

Watch

Duration: 4 minutes 4 seconds4m 4s