Air New Zealand would fly a limited number of repatriation flights via Auckland.
Official advice from the Covid 19 Ministry regarding the one-way bubble is that travel options remain limited.
"Check with your airline about available flights," says the advice. "Your options for travel from New Zealand may be limited as airlines may not have many flights available."
MFAT continues to advise New Zealanders to "not travel to Australia" since the suspension of the two-way bubble in July.
Air New Zealand's chief of customer and sales said it would be unable to operate quarantine-free South Island routes to Australia citing "operational issues".
"The Australian Government has stated that our crew need to have been in the South Island for the preceding 14 days before quarantine-free flying. As our main crew group is based out of Auckland, this is unfortunately not viable," she said.
Customers in the South Island needing to travel to Australia would have to transit via Auckland.
Aviation commentator Irene King told Newstalk ZB that the situation was "confusing for everyone."
"The one-way bubble is a political announcement running up against commercial realities," she said.
She said South Islanders were unlikely to have a two-way bubble with Australia before travel was opened up with Auckland.
"Allowing travellers from Christchurch to travel to Sydney, while not being able to fly to Auckland, is just nonsense."
With additional reporting from Newstalk ZB