There are fears a cruise ship docked in the port of Fremantle that is already responsible for more than 40 coronavirus cases in WA hospitals could be harbouring dozens more, with authorities evacuating the remaining 12 passengers on board.

Key points: The Artania still has 450 crew and about a dozen passengers on board

The Artania still has 450 crew and about a dozen passengers on board It is understood crew have asked to remain in Fremantle until April 14

It is understood crew have asked to remain in Fremantle until April 14 Health authorities fear there could be scores of other infections on the ship

A renewed standoff is brewing over the ship after its operators on Wednesday fought back against government demands that it leave Australian waters.

The Artania has been directed by the Australian Border Force (ABF) to depart Fremantle at the strong urging of the WA Premier, but its crew has responded by saying they want to remain for another two weeks.

About 450 crew members remain on board the ship after most passengers were flown home to Germany on the weekend on charter flights.

WA Health Minister Roger Cook said some of those left on board had reported feeling unwell.

A passenger on the Artania cruise ship disembarks to be transferred to a Perth hotel by bus. ( ABC News )

All remaining passengers were taken off the ship on Wednesday afternoon and taken to the Novotel hotel in Perth's CBD on Transperth buses after being assessed by health authorities.

None of the passengers or crew from the vessel are Australian.

A total of 41 passengers and crew from the Artania are already being treated in West Australian hospitals for COVID-19, with several in life-threatening conditions.

Health authorities were concerned further infections from the passengers taken off the ship on Wednesday and the crew left on board could put increased strain on the WA hospital system.

It is understood the Artania's crew has written to the ABF asking to remain in Fremantle until April 14 and also requesting a thorough cleaning of the ship.

The Artania has been docked at Fremantle Port since last Friday. ( ABC News: Andrew O'Connor )

The two-week timeframe requested by the vessel is being seen as a way to determine whether anyone still on board has coronavirus and to ensure they can be treated if they do.

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Authorities may take over ship: Premier

WA Premier Mark McGowan said he wanted the Artania to leave as quickly as possible, before it was seen as an example for other cruise ships who might see Fremantle as an attractive place to berth.

"I don't want the Artania to serve as an attractor for cruise ships elsewhere," he said.

He said the ship was a Federal Government responsibility and one option could be for federal authorities to take over the ship and move it out.

But Mr McGowan said he remained concerned that the ship could simply turn around and come back again even if it was forced to leave.

"It is a difficult situation. I understand it is very difficult for the Commonwealth Government," he said.

A Home Affairs spokesperson said the Commonwealth and State governments were working together "to ensure that Artania has the ability to depart Australian waters as soon as reasonably practicable".

More cruise ship COVID-19 infections likely

Mr McGowan said the cruise ship situation had been "one of the greatest frustrations of my life" and he wanted "urgency at a Commonwealth level to deal with it and get it [the Artania] away".

WA Chief Health Officer Andrew Robertson warned earlier this week it was likely there would be more Artania COVID-19 infections, given how quickly the virus spread through other cruise ships.

Sick passengers and crew from the Artania were sent to Joondalup Health Campus on Monday. ( ABC News: Herlyn Kaur )

The treatment of foreign nationals in WA hospitals proved highly controversial over the weekend, with the Australian Medical Association blasting initial plans to cater for patients at Hollywood and either Bethesda or The Mount private hospitals.

The bulk of patients were eventually taken to Joondalup's private hospital in Perth's north, with a handful of others too unwell to be transported still being treated at public facilities.

The passengers still on board the vessel had been deemed medically unfit to fly, due to their previous condition.

Mr McGowan said he was only told on Wednesday about the 12 passengers remaining on board.

Question of health, Attorney-General says

Federal Attorney-General Christian Porter told 6PR radio he was not sure why the ship had requested to stay until mid-April, but it was likely due to the health of passengers onboard.

"I don't have a specific briefing about that but, based on the briefings I've got, that is about people getting some form of basic health assistance that would allow them to undertake the journey home," he said.

Mr Porter said authorities had a humanitarian obligation to ensure the health of those on board before their journey back to Germany.

"Everyone agrees that the cruise ship has to leave and it's under a direction to leave," he said.

"The timing of that has to be a judgment around the health of some of the passengers who are unwell or frail, and that's a matter of health assessments and us doing the best that we possibly can in the circumstances."