Over 300 lightning strikes have struck Northland and Auckland since this morning, as a severe weather front moves down the country.
One tornado damaged a dozen or so properties at Coopers Beach in the Far North and another is thought to have hit a shed in Kaiwaka.
Torrential rain has also fallen in places.
Metservice meteorologist Peter Little said there was still a risk of further tornadoes.
"It's very active with a lot of thunder, lightning and also risk of strong wind gusts and tornadoes, along with the very heavy rain," he said.
"By about 1.15pm, there'd been about 91 lightning strikes over Auckland and 219 over Northland. And that's over the land area as well."
From about 4pm, Wellington is expected to be hit by 120km/h winds in exposed places.
"At the moment it's a bit wet but there aren't strong winds. That's certainly going to change by the time for the afternoon commute," Mr Little said.
Air New Zealand said the forecast strong winds were likely to cause disruptions to flights in and out of the capital this afternoon, and urged travellers to check their flights.
A Fire Service spokesman said they had received numerous reports of fire alarms being activated, surface flooding and power lines arcing in Northland and Auckland.
In Kaiwaka, Northland, firefighters were helping after a shed on Settlement Road was damaged by what was reported as a small tornado.
At the small Far North settlement of Cooper's Beach, 10 to 12 houses were damaged by another tornado this morning, with some roofs lifting and properties damaged.
SH1 NORTHERN MWY - FLOODING - 1:10PM— NZTA Akld & Nthlnd (@NZTAAkl) June 5, 2019
The right northbound lane just after the Upper Harbour Hwy on-ramp is CLOSED due to flooding. Please use the two left lanes and slow down when driving through the area. ^MF pic.twitter.com/pQHF4WYchK
Emergency services were alerted just after 10.30am and said there were no reports of serious injuries.
Fire and Emergency shift manager Daniel Nicholson said two crews were there and another from Whangārei was on the way.
"They're investigating the area and the extent of the damage. We haven't had any other reports in the surrounding area of any damaged caused by it."
Coopers Beach residents said it was a very frightening experience. A motel worker described ducking inside to escape the wind which he thought was about 70 to 80 knots.
Bowling club president Jim Nayler said the tornado seemed to go on for about 30 seconds.
"It was just a very loud rumbling noise and gusts of wind. It gave the building a bit of a shake and fetched a lot of leaves off the trees, which got whisked around. It was certainly severe enough to cause structural damage, that's for sure. I thought, 'Are we going to lose a roof here?'"
Surface flooding has also been causing delays on State Highway 1 on Auckland's North Shore.