The threat of Omicron comes as the Delta outbreak continues to appear under control in New Zealand, the ministry revealing 18 new community cases yesterday.
A woman in her 70s who was infected with the virus died at Middlemore Hospital on Monday night.
Sixteen new cases have been identified at the border, including five with the Omicron variant.
Those take the country’s total Omicron cases identified at the border to 54.
Fifty-four people are fighting Covid-19 in hospitals across Auckland, Tauranga, Rotorua and Waikato. Eight people are being treated in intensive care.
Despite the more transmissible Omicron variant raging across the globe, a Ministry of Health spokeswoman said Delta remained the biggest concern.
"For New Zealand, Delta remains our greatest threat at the moment, as it is present in the community."
The modelling work had not yet been completed on what the scale of an Omicron outbreak in New Zealand could be.
The scientific detail on Omicron was in its infancy and the models available before the Christmas holiday period were still being refined, the spokeswoman said.
"Keeping it at the border, by retaining the MIQ system, is buying us time to study Omicron’s effects overseas, while the traffic light system provides the basis for a strong response.
"We know it will get into the community at some point and we’re learning more every day."
The spokeswoman said early signs looked promising Omicron might not be as severe as Delta.
"However, we need a bit more time before we can be confident in this data.
"While we build a better picture of Omicron, implementing the nationwide response system for the severe Delta strain remains the priority."
No-one at the Southern District Health Board was available to speak on whether worst-case scenario planning for a Delta outbreak of up to 900 cases a week was fit for purpose in the event of an Omicron outbreak.
However, primary health organisation WellSouth chief executive Andrew Swanson-Dobbs was confident the South was ready for an outbreak of either variant.
"I believe we are prepared," Mr Swanson-Dobbs said.
It had increased testing capacity and was prepared to manage Covid-19 cases isolating at home.
Covid-19 modeller Prof Michael Plank believed the traffic light system would not be enough to contain Omicron and a return to something the stricter Alert Level 3 or 4 would be needed to restrict its spread.
While modelling was yet to be completed on an Omicron outbreak in New Zealand, the outbreak in Australia was probably the best guide for what it might look like.
That was because, like New Zealand, it had high vaccination rates and did not have a high level of immunity from the rampant Covid-19 outbreaks seen elsewhere in the world.
"Obviously, it’s spreading extremely quickly in several Australian states and so it will be really important to see what happens with hospital numbers there."
