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Megan Woods is trying to reassure New Zealanders after a maintenance worker at an isolation hotel tested positive for Covid-19.
He had no routine contact with guests,  but genome testing shows his strain is the same as a returnee from the US.
The Minister in charge of border isolation and quarantine said the results of the re-tests of Rydges staff and guests would be known today.
"We have a case of a singular worker who has contracted the virus," Woods told Newstalk ZB's Mike Hosking today. "We are still trying to track down why. We know from the genome sequencing it's not connected to the cluster that's happening in Auckland at the moment."
She denied the suggestion the border had leaked or been breached. The man's close contacts had been tested, with negative results.
"It's not the border leaking. We can't even establish a person-to-person contact for how this man did contract this. We have gone through very methodically, through all the evidence, about where he was as a maintenance worker, what rooms he was in. There is absolutely no evidence this is a border leak. Obviously something has happened - we will continue to chase it down."
She said the Government wanted to make doubly sure there was no one else in the chain of transmission.
Hipkins told Parliament yesterday testing had been too slow and gave figures which showed three days after ordering tests, only half of the 10,000 Auckland Airport and Ports of Auckland workers had been swabbed.
"It has not met the very clear expectations of ministers," Hipkins said.
"The decisions of Cabinet were not implemented in a timely or robust manner. That has been both disappointing and frustrating."
Yesterday a full investigation was launched into how a maintenance worker at the Rydges managed isolation hotel was infected with Covid-19 after genome sequencing ruled it out as a connection to the Americold cluster.
The case could indicate a possible second chain of community transmission but officials are confident at this stage it's contained, with the man's close contacts all being isolated and testing negative.
The strain of his infection is the same as a woman who returned from the United States and stayed in the Rydges between July 28 to 31 before being moved to the Jetpark quarantine hotel after testing positive.
Officials reviewed CCTV footage and swipe card records and found there was no obvious person-to-person contact, with the woman only leaving her room two or three times and the maintenance worker not entering it.
Woods said the infection was not related to any incidents or systems breakdown.
"This case highlights how tricky and insidious this virus can be."
All guests and staff at the Rydges Hotel are being tested as officials work to establish how the man was infected.
But it was revealed the man passed two daily health checks and temperature checks despite having a cough because he put it down to a pre-existing condition.
His case was only picked up as a result of the mandatory testing regime on August 13.
Director general of health Ashley Bloomfield said the man's case was believed to be contained with his household and workplace contacts testing negative and being isolated for two weeks.
And as of yesterday morning, 97 per cent of staff at Auckland MIQ facilities had been tested in the hunt for the source of the Americold outbreak which appears to have the first case, with the onset of their symptoms starting on July 31.