A rare atmospheric event so uncommon there have only been two in New Zealand since records began is on its way, and will probably bring cold and unsettled weather with it.

National Institute of Water and Atmospheric Research (NIWA) meteorologist Ben Noll said the Sudden Stratospheric Warming (SSW) was occurring in the atmosphere about 30km above Antarctica and will peak on Friday.

SSW is a heat wave in the stratosphere, which is 30-50km above ground, and can disturb an area called the polar vortex, which usually keeps harsh, wintry conditions locked up close to the South Pole.

"This Sudden Stratospheric Warming can weaken that vortex and that can lead to cold air masses branching off from Antarctica into the middle latitudes and one of the places that could see the impacts could be New Zealand," Mr Noll said.

"It's underway, but it takes quite a while for the impact to translate from the stratosphere, which is way up in the atmosphere down to the ground. We won't see the impact of it on the ground for another few weeks."

However, he said the unsettled and cold weather outlook for the next couple of weeks could be caused by this event, and it will also increase the odds for cooler and stormy weather through September and October.

"We are expecting to see some of that weather later next week and also the following week," Mr Noll said.

"The next several weeks are a very important time of the year for farmers in the South Island, for example lambing season, so keep an eye on daily weather outlooks will be particularly important given the volatility that is expected to occur."

Mr Noll said a major SSW occurred in the Northern Hemisphere in February 2018 and was dubbed the "Beast from the East". It was associated with a series of strong cold waves across Europe.

There have only been two SSW events in New Zealand in recorded times - one in September 2002 and the other in September 2010, according to NIWA.

After the SSW in 2002, New Zealand experienced its coldest October in 20 years with below average temperatures covering much of the country and frequent ground frosts.

In 2010 - which was classed as minor event - a number of rainfall records were broken with well below normal sunshine and very cold temperatures in parts of the South Island, NIWA said.