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The man is in his 60s and is now in a quarantine facility in Auckland - the Jet Park Hotel.
The man flew from Pakistan to Doha and on to Melbourne on June 11, and then to Auckland on Flight NZ124 on June 13. He wore a mask on the flight and developed symptoms on June 15.
The Ministry of Health is in the process of contacting all people on the flight.
There are now 1157 confirmed cases of Covid-19 - 1507 in total, including probable cases.
In a media briefing this afternoon, Director-General of Health Dr Ashley Bloomfield said all passengers on flights from Australia and New Zealand would now be required to wear masks as an additional precaution.
Air NZ crew doing long-haul flights with a layover also now had stricter requirements, Dr Bloomfield said.
"They now have to self-isolate on return and get a negative test result before they are able to return back into the community."
Dr Bloomfield also spoke about the two sisters with Covid-19 who were released from isolation to travel from Auckland to Wellington to visit a dying parent earlier this week.
He said one of the two friends who met with the two women had returned a negative test and the other test was still pending.
He said 90% of the 364 contacts of the two women, who also stayed at the Novotel Hotel in Ellerslie and were on their flight, had been contacted so far.
"There was a lapse in the process for us introducing the routine day three and day 12 testing in the latter part of last week and I know that the case of these two women will have upset people and shaken people's confidence," Bloomfield said.
"When I found that out, I followed up," Dr 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."
Dr Bloomfield said the ministry team and staff and many people working across the health system were 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. I have instructed that no one is to leave the managed isolated hotels unless they have been tested," Dr 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.
He said the two women took the wrong motorway exit 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.
Dr 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.
He said now all would be followed up and checked.
No one now leaves a facility unless they have a confirmed negative test, even if it's under compassionate leave, he said.
Dr 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.
Prime Minister Jacinda Ardern yesterday said the situation with the two women was an unacceptable failure of the system and she appointed assistant chief of defence Air Commodore Darryn Webb to oversee and review managed isolation facilities.
- additional reporting RNZ