Severe thunderstorm watches have been lifted for many regions in the North Island but remain in place for Waikato and Bay of Plenty.
MetService said coasts from Waitomo to Bay of Plenty are at risk of being hit by severe thunderstorms up until 6pm tonight.
Earlier, thunderstorm watch warnings were in place for parts of the country as far south as Buller.
Heavy showers and moderate thunderstorms are still possible over western coasts from northern Westland, said MetService.
There is a chance this weather will continue into Friday they said.
There is also a heavy rain warning in place for Westland.
In Waikato, rural road has been washed out as most of the North Island has come under heavy rain.
A part of Marokopa Rd in Waitomo has been washed out and is no longer passable as the area floods.
MetService said the severe storms could potentially be damaging.
In Auckland this morning, speed limits across the harbour bridge were reduced for just 10 minutes due to strong wind gusts before being relaxed.
Waka Kotahi NZ Transport Agency said it is continuing to monitor the wind speeds.
Meanwhile, the Ruapehu District Council is warning of floodwaters reaching a metre deep.
The council says civil defence and emergency services are at Totara Cres, Matapuna in Taumarunui, where the flooding is at its worst - but no houses have been inundated yet.
"Emergency Services are pumping water away from the area and sandbagging to protect property and contain the flooding, and some residents have voluntarily evacuated from their properties."
State Highway 4 in Taumarunui is closed between Hakiaha St and Okahukura Bridge Rd due to a slip.
Motorists are advised to detour via Okahukura Bridge Rd, Ongarue Back Rd, Golf Rd and Short St.
MetService said downpours of 25-35mm of rain, large hail and gusts up to 110km/h can be expected during these "intense storms".
A line of showers is also headed for Auckland this morning, which is expected to create hazardous road conditions.
Waka Kotahi is preparing to shut down the Harbour Bridge at the slightest sign of trouble, as MetService predicts gale-force winds, hail and torrential rain will lash the upper North Island throughout today.
There's even a chance a tornado will rip through the region, causing damage.
MetService is urging people to be aware of the hazards, saying rainfall and winds of this intensity can cause flash floods and slips, and make driving dangerous.
The storms could become severe from Northland to Taranaki between 6am and 3pm, and Bay of Plenty and Rotorua could see similar conditions between 9am and 4pm.
"Wind gusts of this strength, and damaging tornadoes can cause structural damage, including trees and power lines, and may also make driving hazardous."
In preparation NZTA has put the moveable barrier into the 4/4 lane configuration on the Harbour Bridge, meaning it is ready to shut at any moment.
The unsettled weather stretches further south too, with thunderstorms forecast for Wellington, and the South Island can expect its fair share of unsettled conditions too.
Northern Westland, Buller and northwest Tasman have a moderate risk of thunderstorms during the day, which may be accompanied by localised heavy rain of 15 to 25 mm per hour and hail of 5 to 20mm in diameter.
It's the second day of hectic weather for the lower end of the North Island, after a small tornado tore through the beachside town of Waikanae yesterday.
Roger and Mavis Smith were relaxing in their Waikanae Beach home when a mini-tornado muscled its way across their property in Weggery Drive today.
The drama started at 11.15am when two metal bi-fold doors "blew open and a huge sound erupted", Roger said.
"It sucked the doors out."
The couple's roof was destroyed by the storm, and they described the blast as being "like a bomb going off".
Mayor Wayne Brown unveils the driver safety screens being rolled out on Auckland buses. Video / Carson Bluck