More than 1,300 crew members are being moved between cruise ships in Sydney Harbour in what NSW Police have described as the largest maritime operation the city has seen outside wartime.

Key points: Five Carnival cruise ships will have left Australian waters by tonight

Five Carnival cruise ships will have left Australian waters by tonight NSW Police and the port authority are working to refuel and restock the ships

NSW Police and the port authority are working to refuel and restock the ships The Ruby Princess ship, which saw more than 600 COVID-19 cases, is not part of the operation

Five cruise ships were to be restocked before leaving Australian waters in an operation dubbed 'Operation Nemesis'.

Late last month the Australian Border Force ordered all cruise ships to leave Australian waters before June 15, warning of penalties of up to five years in jail or a $63,000 fine.

The Spectrum of the Seas and Radiance of the Seas ships departed for their home ports after being refuelled and restocked with food and medical supplies just before 2:00pm.

The Celebrity Solstice, Voyager of the Seas and Ovation of the Seas were all set to depart on Saturday night.

Shortly before midnight NSW Police said the operation was ongoing.

"NSW Police has been instrumental in facilitating the movement of more than 750,000 tonnes of shipping through the Port of Sydney over about a 30-hour period," Superintendent Steve Hegarty said.

Crew are being moved between ships depending on where they are heading home to. ( Supplied: NSW Police )

The operation involved NSW Police Force Marine Area Command as well as the NSW Port Authority and Royal Caribbean Cruise Line, the operator of all the ships.

There are no passengers on any of the ships, only crew who have been under quarantine.

It is not known how many crew members have tested positive to coronavirus but several from the Radiance of the Seas were evacuated and taken to hospital this week.

Police working overnight on the cruise ship operation. ( Supplied: NSW Police )

Saturday's operation took place at Athol Bay, near Cremorne Point on Sydney's north shore.

Superintendent Hegarty said they were moving crew members between ships so people were organised according to their destinations.

"It is about getting some of these people on the cruise ships back to their home countries, back with their families," he said.

The coronavirus-hit Ruby Princess has not been listed as part of the group of five and is still on the Sydney coast at Coogee in the south.

Seven coronavirus deaths have been linked to the Ruby Princess, as well as hundreds of cases of COVID-19.

A political stoush continues over the management of the Ruby Princess disembarkation, which saw 2,700 passengers offloaded in Sydney despite many experiencing flu-like symptoms.

More than 660 COVID-19 cases and the deaths of seven people have stemmed from the Ruby Princess.

Carnival Cruises, which operates the Ruby Princess, has been trying to negotiate with the state and federal governments to disembark all crew members who are unnecessary for the safe operation of the ship.

Six crew members from the Ruby Princess had to be taken off the ship and transported to Sydney hospitals earlier this week.

Carnival Cruises said it was unsafe for the ship to leave Australian waters because emergency healthcare will be out of reach.

NSW Police Commissioner Mick Fuller said an external team of specialists would board the Ruby Princess to conduct health assessments of the crew.