Immunisation Advisory Centre founder Dr Nikki Turner says the strain most likely arrived in October.
"It's only got a small single change in the spike protein, so it's very similar to previous ones. It's just become more dominant very rapidly."
Dr Turner said the traditional vaccine was holding up well against the new strain, but an updated vaccine expected to arrive in a few weeks "closely matched" JN.1.
Medsafe approved Pfizer's application for an updated shot for the XBB.1.5 strain in December and it will be available in time for the upcoming winter season.
"American data is showing the vaccine looks highly effective to the strain, so that's very reassuring," Dr Turner said.
She said the new variant was slightly different to the previous one.
"We do have to remember about all vaccines with Covid, they're more effective against severe disease.
"So the vaccines are preventing a lot of severe disease."
Dr Turner said mild disease was expected, even after getting vaccinated.
"But the vaccines are having a very good effect against hospitalisation," she said.
She said the virus was spreading even though people had been spending a lot of time outside thanks to a warm summer.
"Even though we go outdoors, we do mix closely.
"We sit together and cars, we sit together and transport, we cuddle up in our barbecues and, you know, we hug.
"It's pretty easy to spread this little bug around."
Dr Turner said vaccines offered the best form of protection.
"Particularly [for] people who at high risk, you really at this stage still need a vaccine every six months, six months since you had the disease or six months since you had a last vaccine."
The elderly, people with medical issues, those concerned about getting severe flu or Covid symptoms should not delay getting the vaccine, she said.
But Covid was not the only virus we needed to worry about, she said.
"Flu is nasty and it kills."
She said most flu cases were in winter, but recently there had been some non-seasonal outbreaks.
The new flu vaccine would be available in March.
Dr Turner said it was essential people got it, especially because it was updated each year to match the variance.
She said it was safe to get the Covid and the flu vaccine together.
"There is data to show that they are both effective if you have them at the same time. And I'd suggest to many people prior to winter, think about having both of the vaccines at the same time."
