A freak tornado hit Auckland Thursday killing three people and causing "utter devastation" as wild weather ripped apart homes and caused flash flooding in New Zealand's largest city.

The storm, packing gusts of more than 110 kilometres (70 miles) per hour, struck suburban Hobsonville in the afternoon, toppling trees, ripping roofs from houses and sending debris flying.

Civil Defence said three people died and seven were hospitalised, with two of the fatalities believed to have been caused by a concrete slab that landed on the cabin of a truck and the other by a falling tree.

About 150 homes were badly damaged, many rendered uninhabitable, forcing residents into temporary accommodation at a nearby air force base.

Resident Suzanne McFadden said the storm roared through in "five minutes of utter devastation".

"It honestly looks like a bomb has gone off in the street," she told NewstalkZB.

"I saw it coming across the river, the air went very electric and the sky went black. And then the wind started to whistle."

Police urged people to stay indoors as flash floods blocked roads and falling trees brought down power lines, blacking out about 1,300 homes.

Construction worker Sam Nuttall said the storm, which struck at 1:00pm (0000 GMT), came without warning.

"You couldn't see it coming," he told reporters.

"There was debris flying everywhere, steel flying around. Where I was we were sheltering between a big block wall and a truck and there were crates and everything flying at the truck, breaking the windows.

"I've never been in weather like that before."

The Metservice weather agency said the tornado was created by a series of intense thunderstorms that lashed the city through the day, largely dissipating by early evening, although there were fears the winds could pick up overnight.

Prime Minister John Key expressed condolences to the families of the dead and praised the efforts of emergency services, who swiftly sealed off an area of about one square kilometre (0.4 square miles) that was worst affected by the tornado.

"This must have been an extremely frightening situation for many people in the local community," he said.

Another tornado hit the city in May last year, killing one and injuring dozens more as it ripped the roof off a suburban shopping mall.

New Zealand is prone to tornadoes but they are relatively rare and typically much smaller than those seen in North America, where a string of twisters killed dozens of people in the US Midwest last March.

James Renwick, a specialist in atmospheric physics at Wellington's Victoria University, said there was no discernable pattern to tornado activity in New Zealand.

"These events strike at random from time to time, but they are very localised and sporadic and are not obviously tied to trends in the large-scale climate," he said.

"At this stage, we have no indication that tornado occurrences will become more or less frequent in future."