Quarantine-free travel from New Zealand will be suspended until at least Thursday, prompting a rebuke from Prime Minister Jacinda Ardern.
Ms Ardern has told Australian Prime Minister Scott Morrison that she is disappointed by the decision.
"I certainly shared my view that this was a situation that was well under control," she told reporters on Tuesday.
"If we are to enter into a trans-Tasman bubble we will need to give people confidence that we won't see closures at the border that happen with very short notice over incidents we believe can be well managed domestically."
Federal Health Minister Greg Hunt announced the government's decision on Monday.
The suspension came after a woman in New Zealand tested positive for a highly contagious virus strain found in South Africa.
It is the first local case in New Zealand in more than two months.
Australia again recorded zero locally acquired coronavirus cases on Tuesday, with just four cases detected in hotel quarantine.
Acting Chief Medical Officer Michael Kidd told ABC radio on Tuesday that coronavirus vaccines would not trigger wholesale changes to restrictions when the rollout ramps up in coming months.
