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Virgin Australia public affairs manager Kris Taute told the Otago Daily Times the flight, due to land at 4pm, had just a single New Zealand passenger on board.
The return service, to Brisbane, would be repatriating a small number of Australian citizens.
Mr Taute said Queenstown Airport and border security staff would be ensuring that passenger fully understood the official government direction relating to lockdown and isolation as soon as they landed at the airport.
Queenstown Airport corporate and community affairs general manager Sara Irvine said Southern District Health Board staff would be on site at Queenstown Airport for the international flight arrival this afternoon.
The airport was working closely with the DHB, border agencies and the police to ensure protocols for both international arrivals and Covid-19 Alert Level 4 were followed.
This afternoon's flight will be the last scheduled international service from Queenstown Airport for, at this stage, three months.
Meanwhile, New Zealanders stuck aboard the Vasco Da Gama cruise ship off Western Australia are due to be transferred to an Air New Zealand flight home tonight.
Western Australia's Premier says the ship docked at Freemantle Port so the New Zealanders can be taken to an airport.
The Vasco da Gama was involved in a dramatic passenger swap off the coast of Thailand.
Its Europe-bound passengers used lifeboats to get on board another ship, the Columbus, and 108 New Zealanders and dozens of Australians got onto the Vasco da Gama.
- additional reporting RNZ