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MetService forecaster Cameron Coutts confirmed the record was broken when the temperature at the airport reached 35degC shortly after 3pm.
The temperature needed to be verified by Niwa before it was added to the record books, but Mr Coutts said there was no reason to believe it had not beaten the previous high of 34.9degC, recorded on February 26, 1995.
The keeping of records dates back to 1972.
Before hitting 35degC, the airport logged its hottest January day, 34.8degC - beating the previous high of 34.6degC, recorded on January 18, 2004. Another scorcher - 34.1degC - was logged on January 5, 2013.
The hot temperatures were caused by a warm, subtropical flow travelling from the northeast down New Zealand, which was exacerbated by warmer than usual sea temperatures.
Temperatures also got warmer as winds pushed the air over hills and mountains, in a phenomenon known as the foehn effect.
This effect was normally associated with northwest winds, but could also happen in northeast winds.
The heat has set in over much of the country but the South is bearing the brunt, with many places in the high 20s or low 30s around 3pm.
At 3pm, Dunedin city was showing 31.1degC, Alexandra 30.5degC, Queenstown 27.7degC and Wanaka 26.2degC. Of the smaller towns, Millers Flat was leading the way with 32.7degC.
Several places in Canterbury were around 30degC, while most of the North Island was enjoying temperatures in the mid to high 20s
A change may be in store, as MetService has warned Dunedin, Clutha and Southland residents to expect thunderstorms and possible hail this afternoon in the warm, humid northeasterly flow.
The focus of significant convection will shift from the North Island to the southern South Island, where daytime cloud build-ups are expected to produce isolated heavy showers (25mm or more an hour) or thunderstorms to parts of Dunedin, Clutha and Southland.
"There is a moderate risk of a few thunderstorms between Dunedin and Invercargill in the late afternoon and evening.
"If any thunderstorms do develop, they will be accompanied by brief heavy rain and possible hail in the 5mm-15mm diameter range.''
Yesterday, the so-called "Taieri microclimate'' was in full force as temperatures soared to 33.9degC at Dunedin Airport.
MetService meteorologist Tui McInnes said it was the third-hottest January day on record at the airport, before today's reading.
The official MetService thermometer at Dunedin Airport reached 30.1degC at 11.30am, while Dunedin City was still struggling to reach 20degC.
Mr McInnes said the exaggerated difference between the two temperatures was common in the area.
Quite often when the region had warm, fine weather, the land on the Taieri heated up and caused air in the area to rise.
"When the air rises, something has to come in and replace it. So then we get cooler breezes coming from the sea.
"They only go a few kilometres inland, but they tend to drop temperatures in coastal areas [such as Dunedin City] because the sea surface where they come from is generally cooler.''
It was not until about 2pm, when the cooler sea breezes around the coast dropped, that the two temperature gauges started to meet, as Dunedin city headed towards 29degC.
Invercargill again passed the 30degC mark, but did not break its record of 32.3degC, set on Sunday.
Alexandra, Balclutha, Gore and Wanaka also recorded highs of 30degC or more; Queenstown came close with temperatures in the high 20s, and Oamaru recorded the lowest high of the day with just 23.7degC.