Covid-19 Response Minister Chris Hipkins the two new cases in the Taipa area are 'a big puzzle'.
The unlinked cases prompted a snap lockdown last night, dividing the Far North from the lower parts of Te Tai Tokerau still in level 2.
Hipkins says genomic sequencing will help contact tracers, but the mystery cases have not been to any locations of interest or met with people known to have the virus.
"All lines of inquiry are open at this point. Genomic sequencing will help us with that but also we are aiming for some pretty intensive testing today and that'll also help us identify if there are other cases out there."
He says the cases have been 'very cooperative' in contact tracing interviews and have kept 'good records' of their movements.
Fourteen people have tested positive in Northland in the past fortnight.