Whole genome sequencing confirmed the BA.5 variant.
"The person followed all testing and reporting requirements, allowing this new sub-variant to be identified quickly, and has now completed their isolation at home," the ministry said.
This follows the detection of BA.4 in a person who also travelled from South Africa.
The ministry says the arrival of BA.5 is not unexpected and no health setting changes would be required.
"At this stage, the public health settings already in place to manage other Omicron variants are assessed to be appropriate for managing both BA.4 and BA.5."
They said the detection of the variant highlights the importance of rapid antigen testing on arrival to New Zealand on days 0/1 and day 5/6.
The MoH would continue to monitor the emergence of sub-variants closely, they said.
"It can take weeks or months to assess the severity of each new variant or sub-variant, so the Ministry of Health will continue to monitor the emerging evidence closely."
The UK Telegraph reports that South Africa's Covid cases are beginning to soar again because of BA.4 and BA.5, according to scientists.
In the past two weeks, South Africa's daily new cases have gone up sixfold to almost 10,000 a day, with one in every four tests coming back positive. This means the country is now staring down the barrel of a fifth wave.
Today's New Zealand cases are in Northland (129), Auckland (1895), Waikato (353), Bay of Plenty (143), Lakes (77), Hawke's Bay (176), Mid Central (184), Whanganui (69), Taranaki (131), Tairāwhiti (30), Wairarapa (67), Capital and Coast (424), Hutt Valley (206), Nelson Marlborough (189), Canterbury (914), South Canterbury (83), Southern (523), West Coast (51), Unknown (3).
The numbers reported today show that the seven-day rolling average of daily cases has increased slightly since last Sunday.
Today the average is 7510; last Sunday it was 7414.
Of today's reported deaths, two people were from Canterbury and one from Mid Central. Two were aged in their 80s and one was aged over 90.
Today's figures take the total number of publicly reported deaths with Covid-19 to 860.
The seven-day rolling average of reported deaths is 16.
There were 73 cases of Covid-19 detected at the border.
There have been 986,261 cases of Covid-19 recorded in New Zealand since the beginning of the pandemic, including the Prime Minister Jacinda Ardern's partner Clarke Gayford, which put her into home isolation today.
Ardern broke the news of Gayford's positive test and her isolation in a social media post this morning.
She said Gayford "woke up feeling a bit average and has tested positive ... so we have 7 days of family time ahead of us!"
She said she and daughter Neve are "fine".
"I'll be working from home so anyone who watches question time, or is attending my Business NZ speech on Wednesday, you'll still see me remotely."
There are 52,558 active cases in the community.
Yesterday, just 27 first vaccine doses, 43 second doses, six third primary doses, 1256 booster doses, 105 paediatric first doses and 686 paediatric second doses of the vaccine were administered.
Earlier, a report was released by the World Health Organisation which showed that about 15 million people worldwide were killed either by coronavirus or by its impact on overwhelmed health systems in the past two years.
Scientists tasked by WHO to calculate the actual number of Covid-19 deaths between January 2020 and the end of last year estimated there were between 13.3 million and 16.6 million deaths that were either caused directly by the coronavirus or were somehow attributed to the pandemic's impact on health systems, like people with cancer unable to seek treatment when hospitals were full of Covid patients.
The UN agency's chief Tedros Adhanom Ghebreyesus described the figure as "sobering", saying it should prompt countries to invest more in their capacities to quell future health emergencies.
The WHO said it wasn't yet able to break down the figures to distinguish between direct deaths from Covid-19 and others caused by the pandemic, but said a future project examining death certificates would probe this.
Earlier this week, the Ministry of Health reminded Kiwis remain vigilant despite the spread of Omicron slowing.
"With ongoing community transmission across the motu it is important we all remain vigilant.
"Please continue to follow public health advice to stay at home, away from school or work if you're feeling unwell."
A woman who has been ill with Covid for more than a month also warned others not to become complacent.
Along with the well-reported side effects of high fever, brain fog and loss of taste, Auckland woman Clare Jennings said she has had "awful and unusual" symptoms such as a burning smell in her nose, hair loss in chunks and debilitating insomnia.
She has battled ongoing nausea, has lost 8kg and is constantly exhausted.
"It has been a hell of a ride and I want to share my experience because it is definitely not just a cold, which is what I keep hearing," Jennings said.
Yesterday she was told that a historic bout of glandular fever might explain why she has suffered so long.
