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The government is due to share plans of its Omicron preparations in the coming weeks.
Dr Ashley Bloomfield says the declining number of cases in the ongoing Delta outbreak shows the traffic light system has worked well.
But he told Morning Report the system, based on vaccination certificates, is less suited to Omicron.
A person working at an MIQ facility in Auckland tested positive for Covid-19 on Saturday. The following day is was confirmed the person had the Omicron variant.
The worker, who was infectious from 10 January, took two bus services in Auckland and visited a supermarket and four other stores in the city.
Two thirds of the close contacts - 43 people - had so far tested negative for Covid-19, Bloomfield said.
The people who live with the worker had tested negative, he said.
"I think importantly, the household contacts being negative is a good sign. What we're doing now is tracking down all those people who could be contacts ... and those we haven't been able to contact directly we're going around and finding them at their houses."
Bloomfield says those on the bus were much lower risk because of the size of the bus and because people were wearing masks.
With such big outbreaks of Omicron in countries travellers were arriving from, Bloomfield says the pool of potential cases in MIQ was larger.
"But also they're at higher risk of getting infected while on route because there are just so many people travelling who are coming from countries where there are large Omicron outbreaks."
The numbers of cases coming into the country was being watched, he said.
Prime Minister Jacinda Ardern yesterday said it was a "case of when, not if" there was an Omicron outbreak.
New Zealand would move to the red traffic light setting if the variant was spreading in the community, Ardern said.
She said the system was designed to deal with surges, outbreaks and had the possibility of new variants in mind.
Bloomfield said it had clearly served the country well over the summer break.
"If you look at the cases from our ongoing Delta outbreak in the community they continue to decline. I think the seven day average is 20 cases a day now. That's fantastic and that's in the context of the traffic light system."
But, he said, it was key to remember that the traffic light system is based on the role of vaccination and the use of vaccine certificates to restrict people's ability to gather.
"It's quite clear that Omicron does escape vaccinations."
Further advice around the need to strengthen or adjust the traffic light settings was currently being prepared, he said.