Director-General of Health Ashley Bloomfield has confirmed the country's first case of the Omicron variant has been found at a MIQ facility in Christchurch.

Dr Bloomfield confirmed the news in a media conference yesterday.

Watch the press conference here:

Dr Bloomfield said the person arrived in New Zealand on a flight from Germany via Dubai that landed in Auckland. People on that flight were then transferred to Christchurch on a chartered domestic flight.

He said all the people on that flight are in two separate hotels in Christchurch.

"This person was tested on day 1, a positive test result on day 2 was reported - that was on the 12th [of December]. The case was reported on the 13th in our numbers as a case that had come from the border."

Dr Bloomfield said there was one other case that had already been confirmed from that flight on day 0-1 testing, "but the whole genome sequencing on that other case show it's Delta strain".

"We're doing urgent whole genome sequencing on all our cases at the border. We fully expected we would find a case of Omicron and in fact we are treating every border related case as if it were Omicron until proven otherwise."

He said the case was double vaccinated with the Pfizer vaccine and is now in the Sudima Hotel MIQ facility in Christchurch, which also has a quarantine wing.

Dr Bloomfield said today there were good protocols in place "that are designed to stop the virus getting across the border that have served us incredibly well", like with the highly transmissible Delta variant.

The Omicron Covid-19 variant: What you need to know

He said one change made to protocols is that if there were an Omicron case at the border then everybody on that flight would be considered a close contact - on both the international and domestic flights.

Everyone on the floor of the MIQ facility where they were staying would be considered a close contact.

"They complete their full 10 days at the isolation facility at this point while we await further data on Omicron, that's our interim approach."

Bloomfield said returnees could not leave their rooms until day 1 test results were in.When this case was found, they were immediately moved to a quarantine facility, he said.

"We think there's very little risk to others in the MIQ facility, both staff and people who are staying there."

Dr Bloomfield said the incubation period of the Omicron variant was shorter than Delta, so the ministry was confident it would pick up these cases during the seven days' managed isolation.

He said there was no additional risk to Cantabrians at the moment due to this case.

"We have every intention of keeping Omicron out of the country for as long as possible."

But he said New Zealand was "very well prepared" in case Omicron was found in the community.

Initial data suggested Omicron was spreading in a few southern African countries that were then put on the very high risk list, but "that's not particularly helpful, because Omicron is everywhere, really".

Joint Head of MIQ Chris Bunny said the managed isolation facility was well set up to care for these people and protect the community.

"Managed Isolation and Quarantine takes the safety of workers and their families, whānau and broader communities very seriously," Bunny said.

"All Managed Isolation and Quarantine facilities follow strict infection prevention controls developed by the Ministry of Health to manage the risks of spreading Covid-19. The Ministry of Health's advice is to continue with our rigorous MIQ IPC protocols.

"At every MIQ facility returnees must remain physically distant from each other, and from staff members, at all times.

"At a quarantine facility, returnees cannot leave their room freely. They must stay in their room unless they have a medical appointment, are on their specified fresh air or smoking time or there is an emergency, such as a fire or an earthquake.

"Staff wear full PPE when escorting returnees to and from their rooms. Returnees are required to wear PPE in line with Ministry of Health guidelines while outside their room. Health staff conducting health checks wear full PPE (face shield, gown and gloves) and do not enter quarantine rooms.

"The Sudima Christchurch Airport dual-use Managed Isolation and Quarantine facility has a very strict Infection Prevention and Control measures in place developed by the Ministry of Health to manage the risks of spreading Covid-19 - as do all MIQ facilities. The staff at these facilities are experienced in managing and caring for positive cases."

Any further information on the case and next steps will be made available today.