The Director-General of Health says he's advised the Government the border rules are at odds with the new isolation rules.
New Zealand has woken to its first day in phase 3 of the Government's Omicron response plan which means significant changes to isolation.
Under the new rules, only household contacts of cases need to isolate - all other contacts just need to monitor their symptoms.
Household contacts will need to isolate until the person who is positive in the house completes 10 days of isolation. The household contact will need to get a test on day three and day eight, or if symptomatic.
But this rule seems at odds with border rules. From February 28, fully vaccinated Kiwis in Australia will be able to skip managed isolation and quarantine (MIQ) but they must self-isolate for seven days.
When asked about the discrepancy on AM, Director-General of Health Dr Ashley Bloomfield said he is aware and has told the Government.
"We've given some initial advice pointing out exactly what you've said - that actually the public health risk is higher here in the community with what has become quite a rapidly growing Omicron outbreak, compared with those people coming across the border," Bloomfield said on Friday.
"They [Government] will take that advice and get advice from right across Government to see whether there is or isn't a plan to actually change that requirement and I think they will look at that very quickly."
Bloomfield said he discussed the matter with the Government over the last couple of days.
When asked why this discrepancy wasn't anticipated when making the rules for phase 3, Bloomfield said the border decisions were made when it was too early to tell what would happen with the Omicron outbreak.
"Remember the dates around that first day for opening up were set some weeks ago and we didn't, at that time, know how the Omicron outbreak would play out.
"As it transpires here we are just a few days short of the 27th and we are moving to phase 3 so now is exactly the right time to reconsider."
When AM co-host Melissa Chan-Green asked why the Government hadn't changed the rules already, Bloomfield said officials consider advice from many agencies, not just the Ministry of Health.
"Of course our advice is just part of the advice the Government goes through. So there are a range of other organisations and parts of government that are involved… They are also part of providing advice the Government will consider."
Bloomfield said while people coming from overseas do still present a risk of introducing COVID-19 into the community, it is relatively low given it's already spreading throughout the country.
He also said while only household contacts are required to isolate, others should also take appropriate precautions and inform employers if they are in contact with a positive case.
"Under phase 3 the only people here who are required to isolate are household contacts. Of course many people who find out they are contacts will choose to isolate… and they should know so they can take those precautions.
It comes after community cases hit an all time high on Thursday with a whopping 6137 new cases and 205 people in hospital. In comparison just eight new cases were found at the border.