Meteorologist Mmathapelo Makgabutlane says residents in the top and east of the North Island and top and west of the South Island can expect rivers to rise rapidly and surface flooding.
Makgabutlane says some regions have already experienced 18 hours of heavy rain, and Tasman, Buller and Marlborough are in line for the highest rainfalls.
The forecaster is warning it could be a significant rain event for these areas, with a chance that heavy rain warnings in the area could be upgraded to red.
She said the storm was the largest weather system to hit the country this year.
The main rain band was expected to extend into the North Island from late Thursday into Friday, bringing large amounts of rain to northern and western regions.
The heaviest rain was expected overnight in Northland and during Friday morning's commute for Aucklanders,
It would extend to other areas throughout the day, Makgabutlane said.
In the South Island, orange heavy rain warnings are in place for: Tasman, northwest of Motueka; the Buller District; the ranges of Marlborough, including the Marlborough Sounds; the Grey District and Westland north of Hari Hari; the headwaters of the Canterbury lakes and rivers; and the ranges of the Westland District.
The Buller District Council has partially activated its emergency operations centre due to the ongoing downpour.
The district is under an orange heavy rain warning with peak rates of 20 to 30 millimetres per hour possible this afternoon.
Buller Emergency Management says it's continuing to assess the situation and will fully activate the centre if necessary.
The Grey District Council has advised of surface flooding across the region, and said sandbags were available it its Preston Rd yard in Greymouth.
Nelson Tasman Civil Defence says the rain is forecast to be steady, with large volumes accumulating in the ranges.
Niwa this afternoon said river flows would increase dramatically for the upper South Island through Friday morning, and urged people to follow official emergency advice.
In the North Island, Northland, Coromandel, Bay of Plenty and the top of Tairawhiti/Gisborne are under orange heavy rain warnings, while Auckland, Waikato, and Taranaki are under watches.
As well as heavy rain, MetService says strong winds are also set to impact parts of the North Island.
Makgabutlane says the strongest winds are expected in South Taranaki, Taihape, and Whanganui, where a strong wind watch is in place for Friday.
There's also a risk of strong winds for the Chatham Islands from Friday night to Saturday morning, she says.
"It will definitely pay to keep a close eye on metservice.com for updates over the next day or so,” Makgabutlane said.
By the end of Friday, the heaviest rain is expected to have largely moved off the country, though it may linger in eastern Bay of Plenty.
Makgabutlane said the weekend would be mostly dry, but some showers could still affect areas that had already seen heavy rain, especially on Sunday.
