Joint head of MIQ brigadier Rose King said two people fled at 4.45pm on Saturday.
"The fact that people have absconded from two of our facilities is a disappointing and unacceptable breach," she said.
King said an investigation was under way into how these events occurred.
"These facilities are not prisons and these individuals have wilfully absconded. There are rules in place for every single returnee from overseas and now the positive community cases, and we expect people to follow these during their stay in managed isolation or quarantine."
King said "deliberate breaches" put the wider community at risk.
In a separate incident, a person who is required to self-isolate left a West Auckland property on Saturday morning.
Police were notified about 8.30am on Saturday that a person who was subject to a requirement to self-isolate at a residential address in New Lynn had left the address.
Professor Nick Wilson said while Auckland had a level of protection with vaccinations and the current alert level, he said it was still a worry.
"There's two extra layers of protection but this is not how the system is meant to work and although the authorities keep saying 'this isn't a prison' well it should be very high security because this just adds to the stress in the community," he said.
While Wilson believes this situation is not as bad as it could of been, with community transmission currently in Auckland. He said it is obvious the MIQ system isn't working as well as it should.
"It would of been much worse if this was somewhere else in the country where there was no ongoing community tranmission," he said
"It's still not very good the MIQ system should be working much better than this."
