Wellington residents have reported seeing flooding outside Parliament.
Residents said lightning seen across the city was followed by torrential rain just after 8pm.
MetService said there could be downpours of 25 to 40mm/hr to localised areas which may cause surface and/or flash flooding, especially in low-lying areas.
This warning comes a day after the upper North Island was hit by wet and wild weather causing flooding across Auckland and Northland.
On Monday morning, Auckland recorded one of its wettest hours on record as a major thunder and lightning storm caused widespread flooding and chaos across the city and northern regions.
Between 8am and 9am, Auckland's Albany weather station recorded its wettest hour - 76.88mm - on record, said Niwa. "This seems likely to become the wettest hour across the Auckland region on record, but we'll need to scour the record books!"
More than 4000 lightning strikes were recorded in one hour - with 700 in just five minutes. Massive thunderclaps and lightning filled Auckland skies from 7am.
Meanwhile, on the eastern part of the North Island, orange heavy rain warnings have been issued for Hawke's Bay, Gisborne and the Bay of Plenty.
Some 150 to 230mm of rain was expected to accumulate while localised areas might see more rain. MetService was encouraging residents in these areas to drive to the conditions as surface flooding and slips might happen.
