WeatherWatch head analyst Philip Duncan said a very big low had anchored itself on either side of the South Island.
He said the east did not cope well with heavy downpours, which was why there was so much flooding in Canterbury and Otago.
"It's unfortunate that they're getting all this rain today ahead of a very, very cold change that's coming a couple of days after this."
The polar blast would bring heavy snow to the southern and eastern coastlines of both islands later this week, with snow to sea level in the South Island and near to sea level in parts of the North Island.
"Nowhere in New Zealand can escape it. This is such a huge system."
The storm would hit the South Island on Wednesday before spreading north over the entire country on Thursday and Friday. It would ease on Saturday before more rain and wind on Sunday.
Meanwhile, authorities in the South Island are bracing for more flooding as the regions continue to get hammered with rain.
Flooded highways have cut Dunedin off from the north and Civil Defence authorities say homes in the Waitaki may have to be evacuated with rivers running at record highs.
Dozens of roads in the region are flooded and State Highway 1 between Dunedin and Oamaru is closed at several points.
Otago Regional Council water resource scientist scientist Matt Dale said all North Otago rivers except the Shag river had peaked at or near record levels.
In Christchurch, a welfare centre was set up to help people affected by city-wide flooding.
Persistent rain caused traffic chaos in the city, with surface flooding in St Albans, Mairehau, Beckenham, New Brighton, Northwood, Burnside and Sumner.
There have also been road and bridge closures, and water seeping into houses has been reported.
Some schools were forced to close for the day, including Christ the King School in Burnside, Rangiora High School, and Ashley and Sefton primary schools in North Canterbury.
In the Tasman district, where the heavy rain caused a fatal landslip yesterday, a number of roads remain closed due to flooding or slips.
Civil Defence authorities warned that while the rain may be easing, there was still a very real danger of more slips.
A second landslide caused another home to be evacuated in Motueka early today.
Mr Greally said engineers would examine the home this morning to check damage caused by the early morning landslip, and warned others in the Motueka region to leave if they felt unsafe.
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- APNZ / Newstalk ZB