A third person has escaped managed isolation.
The man in his 50s escaped from the Distinction Hotel in Hamilton on Thursday.
On Friday afternoon Minister of Health Chris Hipkins confirmed the man climbed down a fire escape and cut through the fence ties to escape.
"I have been advised there was a police officer on site at the time. These are not high security prisons, there is not a cordon around them - they are hotels," said Hipkins.
A statement from Air Commodore Darryn Webb on Friday said the man escaped the hotel around 6:30pm and returned half an hour later.
He is now in police custody.
Webb blasted the man's actions as "completely unacceptable".
"Managed isolation is a critical part in our defence against COVID-19, and it is up to each and every person entering this country to play their part and abide by the law," he said.
Police and health authorities are scouring CCTV footage to establish who may have been in contact with the man while he wandered the streets of Hamilton. One liquor store on Te Rapa Road was closed for cleaning as police believe the man entered.
Hipkins thanked the owner of the store for his cooperation, saying it will help keep New Zealand safe.
"I want to thank the liquor store owner in Hamilton for their responsible actions - their response will ensure our team of five million remains protected."
The man reportedly bought a four-pack of Leffe Blonde and a bottle of pinot noir. NZME reports he paid in cash, resulting in all of the money in the liquor store register needing to be cleaned on Friday morning.
"Police ensured no one entered the store this morning until health officials confirmed it was safe to do so," said Webb.
Hipkins added CCTV footage from the shop confirmed no other customers were there while the man was.
The man had returned to New Zealand from Sydney on 1 July and had tested negative for COVID-19. He was tested again following his return to the facility and on Friday afternoon Hipkins confirmed the second test was also negative.
"It is important to note that the COVID-19 health risk has been assessed as very low," said Webb.
The man will appear in court later on Friday.
The man's escape is the third in just over a week. On Saturday 4 July a woman scaled two fences to escape from Auckland's Pullman Hotel and was out of isolation for more than an hour.
On Tuesday a 32-year-old man snuck through a gap in the Stamford Plaza fencing and visited an inner city supermarket.
The following day he tested positive for COVID-19.
All three escapees will face charges.
As a result of the breaches in security the Minister in charge of managed isolation, Megan Woods, announced on Thursday all isolation facilities will have a 24/7 police presence to keep people inside and stop the spread of COVID-19.