Passengers on flights from Australia will now be forced to wear masks as officials scramble to recover lost faith in their quarantine system.

The border is paramount in the country's fight against COVID-19 after a 51-day lockdown allowed New Zealand to eliminate the deadly virus.

However, Ms Ardern has installed a military leader to run NZ's border and quarantine regime after admitting she "lost faith" in her health department to do so.

Health officials allowed two citizens out of quarantine early this week without tests, only for them to meet friends against the terms of their release and later return a positive result.

Asked whether she felt let down by the failure, Ms Ardern said "New Zealand feels that at the moment. The whole team of five million feels that".

"Our job is to restore people's confidence."

Health officials cannot say how many tests have been missed, as stories mount of incompetence and intransigence.

"Information evolved," Ashley Bloomfield, the country's top health official, said after presenting incorrect details as fact and apologising.

The Chief Ombudsman has also pledged to investigate after members of his staff came into contact with quarantined individuals at an Auckland hotel.

Other reports suggest Kiwis have been slipping out of quarantine to attend funerals and events.

Opposition health spokesman Michael Woodhouse said a homeless man was able to trick his way into a quarantining group at a five-star hotel.

"He hadn't come back from overseas, he just joined the back of the queue two weeks ago, and spent a fortnight getting three square meals and a bath every day," Mr Woodhouse told Newshub.

"It just shows what a shambles this thing is."

Ms Ardern's government is now scrambling to stay on top of the mess.

Health Minister David Clark, who embarrassed the government during lockdown by mountain biking and visiting a beach against the rules, has repeatedly refused to resign and, like Ms Ardern, is blaming his department.

"The Ministry of Health has failed to do what it said it was going to do. It has failed to carry out its responsibilities," he said.

"I have made it clear that I am unhappy with what has happened. Dr Bloomfield has acknowledged the system has failed."

Despite the bungle, New Zealand remains in a relatively comfortable position as the global pandemic rages abroad.

Just 1507 people have caught the virus in New Zealand and 22 have died.

On Thursday, another man tested positive to COVID-19, but this was an example of the border controls working.

The man, aged in his 60s, was picked up while in quarantine at an Auckland hotel after travelling from Lahore in Pakistan, via Doha and Melbourne.

Authorities are now contact tracing individuals who travelled on Air New Zealand flight NZ124 from Melbourne to Auckland on June 13, though all should be in quarantine if proper procedure is being followed.

Australian Associated Press