A Carnival Australia port agent has told the Ruby Princess special inquiry the ship was supposed to arrive in Sydney at 6am on March 19 but instead arrived at 2.30am.

Dobrila Tokovic told the commission on Wednesday it was her responsibility to collect 13 swabs from the ship's medical centre and take them to a nearby driver.

Three of the tests were positive, but NSW Health officials, who did not board the ship, had already allowed the 2700 passengers to disembark, return to their homes around Australia and self-isolate for 14 days.

The ship has since been linked with 21 deaths and more than 600 positive cases, including an outbreak in Tasmania.

Ms Tokovic said earlier conversations had suggested NSW Health would board the ship as they had done when its previous cruise disembarked in Sydney on March 8.

She was told in the hours before the ship's arrival they would not board, but said she wasn't overly surprised by this decision.

"Having 100 people unwell for the duration of a cruise would not stand out as a significant number where I would go 'oh wow they've got an outbreak'," Ms Tokovic said.

Ms Tokovic also said it was her responsibility to organise an ambulance for two unwell passengers as instructed by the ship's administration officer and onboard doctor.

She said she received a call the previous evening from the doctor, Ilse von Watzdorf, who recommended ambulance personnel take special precautions when treating the patients, who had been swabbed for COVID-19.

The commission also heard from NSW Ambulance's Simeon Pridmore, who was escorted onto the ship by Ms Tokovic to collect one of the two passengers needing an ambulance.

Mr Pridmore said on Wednesday he'd been warned before boarding of COVID-19 concerns and was told 11 other people had been swabbed and were in isolation.

NSW Port Authority senior manager Robert Rybanic also told the hearing Carnival's senior director of port operations Paul Mifsud said "it was business as usual."

"He said that NSW Health had deemed the ship a low risk ship and also that it wasn't a COVID ship and the ambulances weren't related to COVID," Mr Rybanic said.

Commissioner Bret Walker SC questioned how anyone could confirm the Ruby Princess wasn't a "COVID ship" before the swab tests results had come back.

"I just took that as the best information that he had ... I didn't pursue that any further," Mr Rybanic said in response.

Duty harbourmaster that day Cameron Butchart, told the commission he had health and safety concerns in regards to sending a pilot to help the ship dock and offered to "turn it around."

Prime Minister Scott Morrison, meanwhile, on Wednesday said Mr Walker's earlier aggressive questioning of a NSW Health epidemiologist was "out of line".

NSW Health senior epidemiologist Kelly-Anne Ressler was reduced to tears on Tuesday when it was suggested there had been a "reprehensible shortcoming" by the department when passengers were allowed to disembark in Sydney.

"I found that very distressing ... our nurses and doctors and first responders, they're all doing a great job, but also spare a thought for our public health officials," Mr Morrison told 2GB Radio.

"We've got to get to the truth of this stuff but my first blush on that one, and that's not to call into question the independence of the commission, but I found that a bit out of line."

The special commission will continue to hear evidence on Friday and is expected to deliver its final report by mid-August.

The ship is en route to Manila after leaving Port Kembla two weeks ago.

Australian Associated Press