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Air New Zealand's website shows no available flights from Australian cities such as Brisbane, Adelaide, Canberra or Sydney to Auckland until late in the month.
The earliest flight that appears to be available to buy tickets for online flies from Canberra to Auckland on July 27.
The confusion has left Kiwis in Australia in the dark over whether they can urgently return home or not.
One affected New Zealander told The New Zealand Herald they were trying to book tickets to Auckland from Brisbane, without success.
The man, who wished to remain anonymous, is due to start a new job in Auckland at the end of the month and wanted to fly home as soon as possible.
"I looked online for flights from other cities, but there's nothing anywhere," he said.
On Saturday, at least three flights were running services between the two cities, but now there appeared to be none, he said.
"I just don't know what to do. I need to get home."
He said he called the Air New Zealand helpline, but hung up after being kept on hold for over an hour.
Some flights - albeit pricey ones - were listed on the Skyscanner website between the two countries, however none were direct flights.
Services from Sydney to Auckland this weekend involve Air New Zealand and another airline, such as Jetstar or Qantas, with a stop in Melbourne.
But it's unclear whether these would fly, as the airline was under a strict directive that no international passengers were eligible to arrive into Melbourne from July 1 to July 14, as Covid-19 spreads within the local community and a lockdown is enforced.
Last week, Air New Zealand cancelled two return services to Melbourne - NZ123, a cargo only flight, and NZ124 operating with inbound passengers to Auckland.
Flights NZ127 and NZ128 today were also cancelled.
The man had spoken to others online in a similar situation who said they had booked tickets on other websites, such as Skyscanner, only to have their bookings cancelled at the last minute.
Others had their Air New Zealand bookings changed and were unsure if they were able to fly home at all, he said.
Air New Zealand has been contacted for comment.
Meanwhile, Brisbane-bound passengers at Auckland Airport at the weekend were removed from an overloaded Air New Zealand flight.
Police were called to the Customs hall after the passengers became angry when Air New Zealand told them they would have to pay for their accommodation, meals and other costs in quarantine.
Passengers were told they would instead leave New Zealand on Tuesday.
Desiraye Solomon and her daughter, Delia Brown, were on the flight returning to the Gold Coast after visiting her father in Wellington who had suffered a heart attack.
They offered to get off the full flight after the captain advised passengers it was overweight and off-balance, but other passengers were randomly picked off a list, she said.
Solomon said other passengers told they had to leave included an elderly woman, another mother and daughter, a mother with a young child and a group of four male teenagers.
Passengers were then given an Air New Zealand letter signed by an unnamed "airport manager" saying they would have to pay for quarantine accommodation and book their own flights.