The weather system causing nasty conditions across the country is now in a "death spiral" and should wear itself out by tomorrow morning, forecasters say.

Heavy rain has seen floodwaters inundate coastal parts of the South Island and bring thunderstorms to the north over the past 24 hours.

Otago, Dunedin, Timaru and Christchurch have been declared as emergency areas, with at least one river still rising.

Meanwhile, a slip blocked part of State Highway 1 north of Auckland following heavy rain in the region this morning. The highway has since re-opened.

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Auckland was hit with heavy showers, including hail and thunderstorms yesterday, in a month with just two rain-free days so far.

The Metservice said further rain was due to fall today, although showers would ease in the afternoon.

Strong winds were also likely, Metservice forecaster Tuporo Masters said, with strong northwesterlies striking the north, while Wellington would be hit by a strong southerly.

"The winds in Wellington will strengthen up to gale force by the afternoon," Masters said. "It's a very complex situation across the country at the moment, really dynamic."

"The whole system is rotating around the country like a washing machine in a spin cycle."

Rain over Auckland as of 7am Saturday.
Rain over Auckland as of 7am Saturday.

Further south, Canterbury and to a lesser extent Dunedin, would face the remnants of yesterday's storm, bringing more rain to an already sodden region.

Masters said the east coast of the South Island could expect another 50mm today, gradually easing in the afternoon.

"On top of the rain they've already had, that's going to mean they're completely saturated, their catchments are already overwhelmed," he said.

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"It will ease but because the ground is already waterlogged anything on top of what they've had won't help."

WeatherWatch forecaster Phillip Duncan said the low causing the chaos had peaked during Friday and should have "fallen apart" by Sunday.

"The low is now in a death spiral - by that we mean it's spinning and unravelling at the centre, creating a much larger centre as the air pressure rises," he said.

The low was currently centred over Cook Strait area but had a large new calm centre stretching and growing out to the east as the low unwound, he said.

Duncan said a much drier and calmer Sunday is on the way for much of New Zealand.