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Covid-19 Response Minister Chris Hipkins yesterday announced the flights - which were due to begin bringing New Zealanders home from midnight - are being postponed for at least three days.
Returnees will be rebooked from Tuesday, but will now have to spend 14 days in a managed isolation hotel on arrival, although they will not have to pay for their stay.
University of Otago epidemiologist Michael Baker said with the highly contagious Delta variant of Covid-19 spreading so rapidly, trans-Tasman travel needs to be flexible.
"This is all about having a proportionate response to the level of risk in different jurisdictions in Australia, and we can see or get a sense that there's a real concern in New South Wales at the moment about their ability to contain this current outbreak."
Baker said international travel requires control measures including pre-departure testing, stints in managed isolation, and no-fly zones.
He said it shows how vigilant New Zealand needs to be, as the Delta variant takes hold in Australia.
As many as 2500 New Zealanders are trapped across the Tasman after repatriation flights from New South Wales were halted.
The government says travellers should expect to be contacted by airlines in the next 24 hours.
It also expected to free up 1000 MIQ rooms for people travelling from NSW, and will work on releasing more rooms in the near future.
Hipkins yesterday asked those who did not need to return to New Zealand urgently "to hold back", to allow those who urgently need to travel to do so.