The trans-Tasman bubble was set up so people could fly from New Zealand to Australia without needing to spend 14 days in a hotel.
However, Australia's expert medical panel made a decision late on Sunday night to change the system.
It means any New Zealanders that fly into Australia from Monday will have to spend a fortnight in hotel quarantine.
The new rule will remain in place for the next three days before the situation is reassessed.
A statement on the Department of Health website said the pause on quarantine-free travel was decided after a meeting with the Chief Health Officers of Queensland, NSW and Victoria and Australia's Chief Medical Officer, Professor Paul Kelly.
"All people arriving on such flights originating within this three-day period will need to go into 14 days of supervised hotel quarantine," the statement read.
"The Australian Health Protection Principal Committee will consider further updates from New Zealand tomorrow and provide advice."
Professor Kelly had said earlier on Sunday that travel arrangements with New Zealand would not change.
Auckland went into level 3 restrictions from 11:59pm on Sunday while the rest of New Zealand is in alert level 2 for three days until midnight Wednesday 17 February.
The move was announced by Prime Minister Jacinda Ardern after three members of a family living in the South Auckland suburb of Papatoetoe tested positive for Covid-19.
The new cases, a couple and their daughter, are the country's first community transmission since late January when a returned traveller in Northland tested positive after leaving quarantine.
The mother works for laundry and catering company LSG Skychefs, which services planes at the airport. Her main duties at the company involved laundry tasks.
As a precaution, food and beverage on Air New Zealand flights will be suspended for domestic routes.