Australians and New Zealanders who were aboard the deadly hantavirus-hit cruise ship will undergo the first three weeks of their quarantine at the Bullsbrook national resilience centre, just outside Perth.

The flight crew that brings them back to the country will have to join them, Australia’s health minister, Mark Butler, said.

He confirmed a last-minute change of plan will see the six people who had been travelling aboard the MV Hondius spend up to two days in the Netherlands instead of returning direct from Tenerife.

They landed in the Netherlands on Tuesday morning, Australian time, on the first leg of a complex operation to repatriate them, Butler said. There they were greeted – at a safe distance – by Australian ambassador Greg Fench.

They were taken to a quarantine hotel before a charter flight takes them to Australia later this week.

“This is a difficult arrangement to make,” Butler told ABC News on Tuesday morning.

“You’ve got to have crew that are willing to isolate at the end of the flight, you’ve got to have a flight that has some refuelling arrangements put in place between the Netherlands and Australia … And it’s important that we’ve put those quarantine arrangements in place, ready to go when they do land in Australia.”

The government nevertheless expected the four Australians, one permanent resident and one New Zealand citizen to be back in Australia by the end of the week. As of late Monday night, it was understood none of them were displaying symptoms of the virus.

“They’re only able to stay in the Netherlands for a maximum of 48 hours. So, over the next 24 to 48 hours, we expect them to start their flight back to Australia,” Butler said.

Medical personnel will be on board the flight, which is expected to land at RAAF Base Pearce in Perth, according to government advice.

The travellers will then be transported to quarantine facilities at the Bullsbrook national resilience centre, about where they will isolate for the first three weeks of a 42-day quarantine period.

Flight crew will also quarantine at Bullsbrook.

None of the passengers have displayed symptoms of hantavirus, and no other Australian citizens or permanent residents were known to be on board the ship.

The World Health Organization has recommended but not mandated a 42-day quarantine for the travellers due to the long incubation period of hantavirus. The virus can cause flu-like symptoms leading to respiratory arrest and death in some cases.

Butler said Australia’s measures were “probably the strongest quarantine response of any country that is taking passengers back from this cruise ship”.

“Most countries are only requiring their returning citizens to go into some sort of centralised quarantine, like a hospital or a centre like the one we’re using in Western Australia, for two or three days, and then they’ll be released to home quarantine – obviously subject to monitoring arrangements,” he said.

“We’ve decided to go with something stronger than that. We have these purpose-built facilities, including, obviously, over in Perth. We have staff from the critical care and trauma response centre that have experience in supporting people in those facilities, and advice towards the end of that three-week period about what should happen for the remainder of the 42 days.”

Oceanwide Expeditions confirmed on Monday that all guests and some crew who had been on the ship had been either repatriated to their home countries or to the Netherlands. Twenty-five crew members remain on board, as does the body of a German guest who died on the ship on 2 May.