NIWA warns the sudden stratospheric warming (SSW) affecting Antarctica could be the "strongest warming event on record".
It says the event "continues to unfold" and has "set high-temperature records in the stratosphere". And it warns the SSW is already starting to affect New Zealand.
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"Temperatures have been below average month-to-date in the South Island," NIWA says.
"[There is an] increased risk for southerlies in New Zealand into October."
A graph shows just how much stratospheric temperatures have increased compared to the average.
NIWA says an SSW happens when the temperature in the stratosphere - 30 to 50km above the ground - rises by more than 25C, reversing the wind pattern.
The polar vortex of stormy and freezing weather is disrupted, allowing "polar air masses known as streamers" to break off from the weakened vortex. These can cause "unusual or extreme weather".
An SSW in the Arctic in 2018 resulted in a cold wave dubbed the 'Beast from the East' across Europe, Ireland and the UK. Nearly 100 people lost their lives in the ensuing cold and chaos.
When an Antarctic SSW happened in 2002 it resulted in the coldest October for New Zealand in 20 years. Historic NIWA data shows it was on average between 2C and 3C colder than normal from Timaru in the south to Auckland in the north. Invercargill saw its second-highest rainfall on record, and hailstones the size of golf balls fell in Christchurch.
"In 2010 - which is classed as a minor event - a number of rainfall records were broken, with well-below normal sunshine and very cold temperatures in parts of the South Island," said NIWA.
Meanwhile, NIWA scientists down at Scott Base down in Antarctica are preparing for the event by making sure all instruments are in "tip-top shape".