"It's the second case of local [Omicron] transmission we have had in New Zealand so it does indicate we are really on borrowed time with Omicron at the moment," Baker said.
Each case recorded in MIQ increases the risk for border failure, he said.
"I think the most concerning thing is the huge amount of infected people arriving in MIQ every day, that means who have well over 300 active cases sitting in MIQ at the moment in New Zealand.
"We've never had anything like that number before and each additional case increases the risk for border failure," he said.
There are 55 close contacts and so far the Ministry of Health say fifteen of these contacts have already returned a negative test result, including five contacts in Taupō.
"Among the close contacts, are 39 people who were on two bus trips with the case. The MIQ worker on the bus trips was wearing their mask throughout both journeys," officials said.
Whole-genome sequencing has linked the worker to two returnees at MIQ who had arrived from India on January 8.
Looking forward to the coming weeks, Baker said the Delta variant could be eliminated in the coming weeks.
"Based on the current trend we could see the Delta variant eliminated in New Zealand in a few weeks time because we are seeing different chains of transmission around of new Zealand basically being stamped out," he said.
Baker said the reason the daily number of cases is dropping is due to the fact over 90 per cent of the population are partially or fully vaccinated.
However, New Zealand now faces the threat of the Omicron variant, which may soon be introduced in the community Baker said.
"We want to delay that for a period hopefully into march or even a bit beyond to give New Zealanders the chance to get boosted and vaccinate children in New Zealand.
"And also just prepare for what will be a very intense outbreak when it does actually arrive here," he said.
Prior to the Delta community outbreak, Baker said the period of time where little to no Delta cases were recorded was due to the low numbers of returnees in MIQ.
"If can turn down the tap and reduce the number of infective people arriving in New Zealand we can make MIQ quite effective."
While there are milder symptoms, Baker said as it is a highly infectious strain of Covid-19 the country will see a "very intense rise of cases".
With the threat of an Omicron outbreak, Baker said New Zealanders should start purchasing high-quality masks.
"Think about upgrading your mask from a fabric one, which is okay in some situations but is not quite good enough anymore if you are going to be indoors with other people who may have been infected."
Baker believes an announcement this week Cabinet will include an alert change for Northland which is currently the only region in the country that has remained in the red alert.
However, he said with the threat of Omicron it is unlikely the rest of the country will move down to the green alert.
"The question now will be much more on preparing for Omicron, I think will be a much greater threat for New Zealand at present."
