Stranded Australians promised free quarantine on return face $5,000 government bill

Stranded Australians who were promised their hotel quarantine fees in Sydney would be waived if they flew home on tickets booked before 13 July are now being told by the government to pay for their 14-day stay in Darwin – in some cases more than $5,000 – after the commercial flight they booked was cancelled.

Some stranded Australians have been forced to decline seats on specially organised government repatriation flights after being told the free quarantine stays are “not applicable” if they accept the government’s offer to repatriate them via the Howard Springs quarantine camp.

One family of four who have been stranded in Italy for more than five months after their commercial flight to Sydney was cancelled have been told by both the Northern Territory and federal governments they will have to pay $5,000 for their two-week stay at the Howard Springs centre in the territory.

Related: Stranded Australians face longer wait as PM declares hotel quarantine alternatives unsafe

A health department spokesman confirmed the federal government would not honour free quarantine promised to returning Australians who had booked on commercial flights before July.

The family booked their flight home to Sydney before the 13 July cutoff, but after the flight was indefinitely cancelled the family registered for repatriation flights, which will cost them more than $8,000 for four one-way fares from Frankfurt to Darwin, scheduled to depart on 12 December.

Guardian Australia understands government officials were unprepared for some of those returning on the evacuation flights to have been stranded for so long that their original flights made them eligible for free hotel quarantine.

The federal health department’s quarantine assistance team is advising that “fee reduction programs operating by state and territory government are not applicable to the accommodation at the Northern Territory centre … at Howard Springs”.

Only a small number of the estimated 36,785 Australians registered as being stuck overseas and unable to return home have been offered places on the repatriation flights.

An NT Health spokeswoman told Guardian Australia the decision to charge or exempt people for quarantine costs was one for the federal health department, but the territory was responsible for sending invoices and collecting payment on behalf of the commonwealth.

The federal Department of Health referred the inquiry to the office of the health minister, Greg Hunt. From there, Guardian Australia understands, the office of the foreign minister, Marise Payne, was consulted.

Last week, 10 new government-facilitated Qantas repatriation flights were announced, from new cities including Frankfurt, Paris and Chennai.

Related: Victoria's new hotel quarantine program may employ 'fly-in-fly-out' staff who live on site

Despite Scott Morrison’s suggestion that all 26,700 Australians overseas registered by mid-September could be home by Christmas, details of 10 new Qantas repatriation flights reveal just one will reach Australia in time for Christmas at home, with passengers of a further three to spend the holiday in hotel quarantine.

The family of four who contacted Guardian Australia have requested anonymity out of concern they will be blacklisted from future flights organised by the Department of Foreign Affairs and Trade (Dfat).

However, the mother of the family said they faced “unfair” costs of at least $13,000 to take the flights.

“I have to decline the flight, not due to unwillingness to return but due to inability to afford,” she said.

She also faces the cost of accommodation at a Frankfurt airport hotel, as Dfat advice for the flight states the family need to test negative for Covid-19 at the airport, but if the family leaves the airport while waiting for their result after landing from Italy and departing for Darwin, they will be forced to quarantine in Germany for 10 days.