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.
"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."