The Ministry of Health is in the process of contacting all people on the flight.
Director-general of health Ashley Bloomfield held a press conference in Wellington.
He said the Ministry of Health would now advise that medical grade masks should be offered to passengers on international flights - and they should be strongly encouraged to use these masks as a precautionary measure while on board.
The masks should come with instructions for proper use, alongside crew instructions in the safety briefing. Hand sanitiser should also be made available on the flight.
Bloomfield said Air NZ crew doing long-haul flights with a layover also now have stricter requirements.
"They now have to self-isolate on return and get a negative test result before they are able to return back into the community."
New Zealand now has 1157 confirmed cases of Covid-19 - 1507 in total, including probable cases.
It was revealed on Tuesday that two sisters who later tested positive for the virus were allowed to leave managed isolation in Auckland to travel to Wellington after their mother had died.
After interviews with contact-tracing staff, more than 300 close contacts of the pair have been identified and will be tested, including other people in the hotel in which they had been isolating and other passengers and crew on their flight from Brisbane.
Bloomfield said he did not know exactly how many of the 364 contacts of the two women had been tested, saying he understood it was the "vast majority".
After leaving the hotel, the two women had contact with two friends who have also isolated themselves and have been tested. One had a negative result and the other is still waiting for her result.
The public health unit routinely do follow-up interviews, especially in a situation where people are distressed, he said.
Neither woman recalled they had brief physical contact with anyone and so the public health unit didn't feel the need to report that.
"When I found that out, I followed up," Bloomfield said.
"As soon as I became clear of what had happened, I released a statement last night.
"Yes, the situation has changed, and I've been open about that."
Bloomfield said clearly the ministry team and staff, and many people working across the health system, are very committed to keeping New Zealanders safe.
"The case of these two women will have upset people, I am certainly upset by it," he said.
"I apologise that we've ended up in this position," Bloomfield said.
"I have instructed that no one is to leave the managed isolated hotels unless they have been tested," Bloomfield said.
He said he had not gone back to check with the women if anything else had been missed but said the public health unit had.
Bloomfield confirmed the two women took the wrong motorway and headed north "partly due to the stressful circumstances on them".
"They ended up travelling north, rather than south, which if you haven't lived in Auckland can be done."
He said one of the people who went to help the duo had put their "arm around them" and said that was the only contact they had.
Bloomfield said he couldn't say how many of the 200 people granted compassion leave were tested before they were allowed to leave quarantine facilities.
No one now leaves a facility unless they have a confirmed negative test, even if it's under compassionate leave, he said.
Bloomfield said he was not concerned there were community clusters we don't know about because all the new cases are related to the border.
"So, I don't see that there could be."
He doesn't know how many people haven't been tested before leaving managed isolation sites since June 9. He said he has asked his team why this hadn't been rolled out - that had been his expectation.
"Over the last few months, our team has dealt with hundreds of compassionate leave applications - some of which have been profiled in the media and have been very tragic."
He said every application went through a rigorous process and he felt confident with the decision made to approve that application.
There is no legal issue to test people in managed quarantined, he said.
"Under the current order, they can be required to be tested and we have made this really clear," Bloomfield said.
Bloomfield said we will see more of these cases at the border.
"Remember the number of cases worldwide is still growing and more New Zealanders will be returning so we do expect to see more cases at the border," he said.
Bloomfield is also expected to face further questions about when he and health officials first suspected that the pair's story that they had had no contact during their car journey was not true.
National MP Michael Woodhouse revealed yesterday afternoon that they had met up with friends after getting lost on their way out of Auckland.
That was subsequently confirmed last night by the Ministry of Health.
Before that, Prime Minister Jacinda Ardern and Bloomfield repeatedly told the public that the pair had had no contact with others on their drive south.
Ardern yesterday announced that Air Commodore Digby Webb would be placed in command of the managed isolation regime.
Compassionate leave for anyone in quarantine or managed isolation has been suspended.
Bloomfield announced on June 9 that all people in isolation and quarantine would be tested at three days and 12 days - just before their release at 14 days.