Dr Ashley Bloomfield says public health teams are no longer pouring resource into finding the links between cases and the focus is now trying to isolate cases and find their contacts.
In an interview with Mike Hosking, the director general of health said he is no longer "obsessing" over numbers of unlinked cases but the contact tracing efforts will continue.
"At this stage we're not putting too much resource in finding out where these cases were infected. The main effort is get these cases isolated as quickly as possible and find their contacts."
He says vaccination is the best way to get the stringent Covid-19 restrictions loosened.
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"What's clear is that despite our very best efforts, we've not been able to get to zero in Auckland so we're staying in alert level 3, we're continuing to chase cases and we're going after vaccination."
He urged people not to panic, despite acknowledging the situation is concerning.
"People should be following the rules and if they haven't been vaccinated, they should do that because that was always going to be our ticket to more freedom - and the future has come forward."
On a potential change in alert level position for Auckland on Monday, Bloomfield said vaccination rates in Auckland would be a big factor in that decision.
That's the hope for Super Saturday, he said. While it might not make a "material difference" for this Monday, it was crucial for down the track. If the vaccination rate reached above 90 per cent then all options were on.
"The sooner we get to 90 per cent, the sooner things can start to free up and that's what we all want."