It will comes as a significant relief for the WA government, who have made no secret of wanting the ship to leave as soon as possible.
A total of 79 crew and passengers from the Artania have tested positive to coronavirus in WA.
They include a 42-year-old crewman from the Philippines who died in a Perth hospital on Thursday, taking the state's toll to seven.
The ship's captain, Morten Hansen, said the crew member had been with the company since 2006 and most recently served as a motorman, describing his death as "heartbreaking".
Two other people from the Artania died last week, one a passenger aged in his 70s and the other a 69-year-old crewman.
Some of the crew who are expected to return home on a charter flight were removed from the ship on Saturday and transferred to a Perth hotel.
It's understood the ship will make stops in Indonesia and the Philippines en route to Germany.
The ship had been scheduled to depart earlier this month before being granted an additional 14-day quarantine period by the Australian Border Force.
Some 219 of WA's 541 cases have been among people linked to cruise ships.
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If you believe you may have contracted the virus, call your doctor (don’t visit) or contact the national Coronavirus Health Information Hotline on 1800 020 080. If you are struggling to breathe or experiencing a medical emergency, call 000.
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