Dr Ashley Bloomfield wants mandatory mask use on public transport, but says the Government's not so keen.
He made his position clear when asked about a New Zealand Defence Force (NZDF) staff member who didn't wear a mask on a plane. They flew after meeting with someone who worked at a quarantine centre, and later tested positive for COVID-19.
It was 10am in central Wellington and health teams were on the case - residents keen to get tested after reports that the NZDF staffer ate at popular eatery Little Penang on The Terrace.
"I'm just not feeling that good and have a friend who works at Little Panang, so didn't want to take any risks," one person told Newshub.
"I'm doing what I've been told to do - go and get tested because I'm feeling sick," said another.
Two NZDF employees have the virus. Employee A has 242 casual contacts - almost all have returned negative tests - and 25 close contacts.
One of those contacts is Employee B - the second NZDF staffer to test positive - who has 55 close contacts of their own.
Defence House, where Employee B worked, was closed on Monday, meaning 1300 people worked from home.
Little Panang was closed for cleaning but has now reopened.
"[It's] life as normal. That's the instruction I got from the Ministry of Health because this is a casual contact and the risk is low," said owner Tee Phee.
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But Wellington mother, Nicki Clark, says the instructions her family received were nothing but confusing.
"I know the situation changes every day, and the advice changes every minute. But get the basics right," she said.
She's dropping meals to her husband, who's isolating at home. He was sitting in the same row on a plane as employee B.
Authorities said initially he was a casual contact, then a close contact - and then the advice changed again. He was a casual contact.
"We've put ourselves in isolation regardless because I don't really trust any of the information," Clark said.
Dr Bloomfield admitted there was conflicting advice, and the person "did exactly the right thing - they clarified with the original advice that they had received".
The latest outbreak started at the country's only dedicated quarantine site, the Jet Park Hotel in Auckland. An NZDF staff member working there tested positive on Friday.
That person then passed the virus on to another NZDF employee, who flew to Wellington. It's the seventh systems failure since August - most cases relate to issues at our MIQ hotels.
"There is a pattern," said Professor Michael Baker of Otago University's Department of Public Health. "I mean this is the weak spot in New Zealand's defences against this virus."
Professor Baker's proposing a new traffic light quarantine system, including quarantine-free travel but tests on arrival for people from places like COVID-free Pacific nations and some states in Australia.
For people from places like Japan, South Korea and Singapore, quarantine could be shorter, with some isolation spent at home.
And for high-risk countries like the US, UK, Russia and India, he suggests people quarantine for a few days before leaving for New Zealand and produce a negative result before getting on the flight.
"It reduces the number of infected people coming into these facilities, and that will reduce the number of border failures. The other thing it could do is divert low-risk travellers away from the facilities," he said.
The Health Ministry also revealed that Employee B, who flew to Wellington, did not wear a mask while on the plane.
"Our advice has been we think there is a case for making them mandatory under alert level 1. To date, that's not the decision the Government has made," Dr Bloomfield said.
Professor Baker says given the heightened risk currently, masks on public transport should be compulsory.
A spokesperson for the NZDF told Newshub staff following what the Government currently advises in level 1 - masks are encouraged but not mandated.
"Additionally, our people are told consistently to not travel or go out in public if they are unwell," the spokesperson said.