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One extreme is expected to be replaced with another later this week, with the MetService predicting the South Island will bear the brunt of a storm which could bring strong winds and flooding.
The forecast extreme weather comes as the heatwave continued today, with Cromwell recording 36.6degC, which was the hottest temperature in New Zealand and equal to the town's January record.
MetService forecaster Brian Mercer said Central Otago was again among the hottest places to be in New Zealand today, with 33.8degC recorded in Alexandra.
It was also hot elsewhere in Otago, with Wanaka reaching 33.4degC, Ranfurly 33.3degC, Queenstown 32degC and Dunedin 27degC.
However, Mr Mercer warned that after more hot days tomorrow and Wednesday, the South Island, including the whole of Otago, was expected to be hit by "quite a significant" storm heading New Zealand's direction.
"It's currently a tropical cyclone, by the time it gets here it will have been downgraded, but it will have strong winds and heavy rain."
Heavy rain warnings were likely and flooding possible.
"Probably most of the country will get heavy rain warnings, or at least a watch for Thursday and Friday."
It was a good time for people to check their gutters and drains.
"Because it's so long since there has been significant rain there could well be a lot of debris [in them]."
At present it was expected to hit New Zealand on the West Coast, near Hokitika, on Thursday, but there was some uncertainty over what track it would take.
"The low-pressure system itself it will skirt the west of the North Island and cross Westland, the strongest winds and heavy rain will be on the west of the South Island."
From Kaikoura down to the Clutha was expected to be the worst hit on the East Coast.
The storm was expected to bring strong northerlies to northwesterlies, which would be followed by a strong, relatively cold, southerly change also expected to bring heavy rain.
The southerly change was expected to "move off quite quickly" and should have mostly cleared off by the end of Friday.