With some two-thirds of Australia's 3,000 COVID-19 cases still linked to overseas travel, Scott Morrison said 14-day home quarantines would now be actively policed with the help of the military.

Thousands of citizens and residents are still arriving in Australia every day and there have been instances of return travellers repeatedly breaking a promise to stay at home.

Morrison said all returnees arriving after midnight Saturday would now be kept in hotels in the city of arrival for the duration of their quarantine.

Those already on Australian soil and under orders to self-quarantine for two weeks will face active checks, he said.

Quarantine measures will be getting "a lot tougher and a lot stricter," Morrison said, adding the Australian Defence Force would "assist in the compliance with these arrangements."

Police in New South Wales this week said they found a 65-year-old woman breaking quarantine twice after returning from Bali. She was slapped with two $1,000 (US$610) fines.

Australia has struggled in particular to deal with returning cruise ship passengers.

Around 200 of the 2,700 passengers who were allowed to disembark one ship in central Sydney without testing have subsequently tested positive for COVID-19.

The presence of three other cruise ships off the coast of Western Australia has sparked an intense debate about whether they should be allowed to dock.

Tens of thousands of Australians are still believed to be overseas and Morrison said it would become harder for them to come home.

He indicated efforts would be made to return some trapped in locations like Peru, but those who departed after the government advised against all foreign travel may be on their own.