NIWA warns the 'sudden stratospheric warming' (SSW) event will peak this Friday, potentially sending a cold blast towards New Zealand in early September.
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"A sudden stratospheric warming event is still forecast to peak on Friday 30 August over Antarctica," NIWA tweeted.
"Impacts take time to trickle down through the atmosphere, but particularly unsettled weather conditions may unfold around NZ starting in the 1st or 2nd week of September."
NIWA says a 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".
NIWA meteorologist Ben Noll says it looks like the biggest impacts from SSW will hit South America first.
"A major warming event is about to unfold, lasting into early September," he says on Twitter.
"The polar vortex will be due south of South America this weekend into early next week - looks quite cold for Chile and Argentina."
When an Antarctic SSW happened in 2002 it resulted in the coldest October 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 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".