Acting Chief Medical Officer Michael Kidd said the new positive tests for the South African strain of coronavirus, a "variant of concern", led to the call.

"This allows continuing protection of the people of Australia while the extent of the situation in New Zealand continues to be clarified," Dr Kidd said, apologising for any disrupted plans.

The Australian government made the decision on advice from the Australian Health Protection Principal Committee on Thursday.

Kiwi health authorities believe the three cases were transmitted at one hotel quarantine facility, the Pullman Hotel in Auckland.

Despite the positive tests, there is still no evidence of community transmission in New Zealand, and the government has no plans to raise alert levels.

Dr Kidd revealed that 12 people who were at the Pullman Hotel had in fact travelled to Sydney before the "green zone travel" arrangements were suspended, with a smaller number travelling on to other states.

"All these people are being followed up by the health authorities in the state where they landed," he said.

The travel suspension will last until 2pm AEDT on Sunday, by which time a further decision will be taken.

Earlier in the week, New Zealand Prime Minister Jacinda Ardern suggested Australia's move was a setback to the goal of a trans-Tasman bubble, saying she had confidence in her health authorities to keep the cases under control.

On Thursday, Ms Ardern reaffirmed her commitment to opening a bubble - which would see people moving freely across the Tasman in both directions without quarantine - by the end of March.

"We still hold that ambition," she said in Auckland.

Ms Ardern says New Zealand will pursue quarantine-free travel with individual states if a whole-of-Australia approach cannot be found.

Australian Associated Press