The Ministry of Health has confirmed that a border-related case with the Omicron variant was briefly active in the community in the Auckland CBD earlier this week.

The individual was in Auckland CBD on 26 December and 27 December, and the ministry says there is risk of transmission to unknown members of the public.

Whole genome sequencing has now found the case to be of the Omicron variant, the ministry said in a statement.

"The case is a recent international arrival who returned a positive result on day nine of their self-isolation period. They had previously returned three negative tests for Covid-19 while completing 7 days of managed isolation at a facility in Auckland.

"The case arrived on a flight from the United Kingdom via Doha on 16 December and is fully vaccinated with a mRNA vaccine. No other Covid-19 infections have been identified from the individual's flight. Investigations are underway as to the source of the infection.

"The result of their day nine test was received on 27 December and they were immediately transferred to an Auckland MIQ facility on the same day. At this point whole genome sequencing was carried out and confirmed the Omicron variant."

A number of close contacts have been identified and those tested have returned negative test results.

Locations of interest include the Impala nightclub on Shortland Street, the Sunny town restaurant, Partridge jewellers, Ahi Restaurant and Soul Bar.

Some attendees have been identified as close contacts and will be contacted by public health.

The Ministry of Health said it was taking the situation seriously and taking a precautionary approach.

"However, we do not believe that the individual was highly infectious at the time of the above exposure events."

It is encouraging all Aucklanders to check the Locations of Interest website regularly and follow the advice provided.

"We have been doing everything we can to prepare for Omicron and to keep it out of the community since the variant was first identified. This has included undertaking whole genome sequencing on every PCR sample taken from Covid-19 cases detected in international arrivals."

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

There were 46 new community cases reported in New Zealand today.