They are not Air New Zealand employees, the national carrier confirmed to the Herald.
It is unclear where the crew members arrived from, and where they are isolating.
The Ministry of Health has been approached for comment.
Air crew members are required to be tested every seven days, advice published by the Ministry said.
From October 2020, overseas-based aircrew were required to stay in a managed isolation facility for the duration of their layover while in New Zealand.
Overseas-based aircrew can leave the managed isolation facility prior to their departing flight from New Zealand, the Ministry website states.
There have been no cases of the Omicron variant yet in New Zealand.
Epidemiologist Michael Baker said the likelihood of the flight crew members transmitting Omicron into the community is low.
But he said very soon Omicron cases will be cropping up in MIQ facilities.
"We'd expect to see people turning up to MIQ testing positive for Omicron any time, that's just inevitable but it's not inevitable that it gets established in New Zealand.
"In a way we are now back to the pre-Delta era or back to the elimination era, in terms of Omicron. W want to keep it out and we want to stamp it out.
"We are not following the suppression approach of that virus."
Australia recorded its first cases of Omicron last month - two people who flew into Sydney from southern Africa on November 27 were infected with the strain.
The variant has since spread to multiple Australian states, prompting questions about the Government's plan to begin re-opening the New Zealand border in January.
Baker said the variant will give the Government much cause for thought.
"The big thing to work out is, what is the scale of risk from this new variant?
"We know it can compete with Delta, not necessarily the transmissibility but it can evade some protection people have, so it means it's effective reproduction number is higher."
New Zealand citizens and residents returning from Australia will be allowed to bypass MIQ from January 17.
But Prime Minister Jacinda Ardern said key travel dates will be reviewed at a meeting just over a week before then.
The latest information on Omicron will be assessed on about January 7 or 8 and adjustments made if necessary, Ardern said.
"If we roll forward self-isolation when Omicron is dominant in Australia, it will effectively be the start of Omicron here."
Ardern said the severity of any variant, and the impact of existing vaccines would be assessed.
Last week, the UK Health Security Agency predicted that B.1.1.529, as its coded, wasn't just likely to better Delta at household transmission, but also in secondary attack rates and growth rates.
That key growth advantage could be down to higher transmissibility, increased immune evasion, or just some combination of the two.
While not yet confirmed, early data indicated a greater risk of re-infection – or the ability to get around immunity from prior infection with earlier strains.
