After the wettest July on record, forecasters MetService say an "atmospheric river" has descended from the north and is drenching the country from tip to tail.
The worst-hit city so far is Nelson, where rainfall has destroyed roads, ruined homes, leading to a state of emergency.
Emergency Management Minister Kieran McAnulty flew into Nelson on Thursday to visit affected areas.
"We were literally watching a hill just flow on down. It was like you were pouring out yoghurt out of a container, just a thick sludge just carrying on down, steady as," he said.
"I've only been here a few hours but I've seen enough to see that there is some extensive damage around this city."
Mr McMcAnulty said more than 300 homes had been evacuated, including 10 due to a landslip.
Of those assessed so far, one in five homes either needs serious repairs or is uninhabitable.
Authorities hope to complete assessments by Friday, though more rain is forecast.
Returning to inspect her property on Thursday morning, resident Maggie Grey told Radio NZ there was an inch-thick sludge in her home.
"I don't know what to expect given the weather isn't over yet," she said.
Emergency management spokesman Alec Louverdis said the monster rain was a "one-in-80 to one-in-100 year event", but future forecasts were not as grim.
"We have a lot of intel behind us ... all indications are that its not going to be as drastic," he said.
Mayor Rachel Reese said the rain was "really devastating" and the repair work "is going to be a long-haul".
Forecasters MetService originally missed the impact to Nelson.
On Tuesday, it issued a rare red warning, saved for the most damaging weather events, for Buller and Westland on the west coast of South Island, adding Nelson to the list late on Wednesday.
Nelson is one of the sunniest regions of New Zealand, receiving an average of 960mm of rainfall each year.
It was soaked by 89mm on Wednesday alone, with predictions of 200mm more this week.
In oft-soaked Westport, which received 70mm on Wednesday, about 160 households were encouraged to "self-evacuate as a precaution" by civil defence.
Another front is due to arrive on Friday.
"This is a chance to take a breath and set ourselves up for what comes next ... don't get rid of those sandbags yet!" Buller Emergency Management posted on Facebook.
The system has also brought heavy rain and savage winds to Northland, north of Auckland, where flooding has closed highways, cutting off the northern tip of the country.
Under La Nina conditions, climate agency NIWA said last month was New Zealand's wettest July on record.
Christchurch suffered its wettest month on record, with three major rains bringing floods and about six months' average rainfall to the Garden City.