New Zealanders in Papua New Guinea and the Solomon Islands could find themselves stranded with no transit through Australia when the travel bubble starts.
There are no direct flights home for those wanting to return from the Pacific nations, where more than 100 New Zealanders are registered with SafeTravel.
The travel bubble officially begins at 11:59pm on Sunday. There will be 'green zone' flights that only carry passengers who have come from Australia, and are flown by crew who have not been on any high-risk routes for a set period of time.
Anyone transiting through Australia needs permission to complete 14 days of managed isolation there before boarding a flight.
"To take one of these green flights, travellers would need to have permission to enter Australia and complete 14 days of MIQ there before boarding," the Ministry of Foreign Affairs and Trade (MFAT) said.
MFAT said it had contacted those registered with SafeTravel, and had also "received a small number of enquiries from New Zealanders in Papua New Guinea and Solomon Islands about how to transit through Australia".
"Officials are currently in discussions with Australia to find a possible solution for those who can no longer transit due to the cessation of red flights by airlines," a ministry spokesperson said.
"The Commissioner of the Australian Border Force may grant an exemption to allow a traveller to enter managed isolation in Australia on the basis of a compelling and compassionate reason to travel."
MFAT has posts in Port Moresby, Papua New Guinea and Honiara, Solomon Islands, which remain open.
The spokesperson said a small number of staff had recently returned from Papua New Guinea and the Solomon Islands in accordance with pre-scheduled travel, which was not in response to the border changes.
MFAT said New Zealanders are advised not to travel overseas at this time, except to Australia from Monday.