Multiple roads are blocked in Hutt Central after extensive damage by weather, with multiple reports of trees down over roads, glass across roads, and extensive damage to roofs, windows and cars, police say.

People are advised to avoid the area.

Additionally, two people are in hospital, and one is in a serious condition, after suffering injuries during wild weather in Wellington this afternoon.

The severe thunderstorm warning for Wellington has been lifted. Earlier, flights in and out of Wellington were suspended.

As of 5.20pm, no more warnings were in place. Watches remained for Gisborne, Hawkes Bay, Manawatu, Tararua, Kapiti-Horowhenua, Wairarapa, Wellington and Marlborough, and a strong wind watch for Hawke's Bay south of Hastings and the Tararua District. The watch will be in place until at least 9pm.

Earlier, eyewitnesses described a tornado whipping through the Hutt Valley as heavy rain, hail and thunderstorms lashed the capital.

Windows were blown out of a bus in Lower Hutt, but no one was hurt.

The storm front hit the region after battering Canterbury earlier this morning, and moved up the east coast of the country.

In Christchurch, Fire and Emergency New Zealand said heavy rain flooded houses in the suburbs of Belfast and Middleton.

MetService meteorologist Lewis Ferris said the storm was moving north.

"The concentration of the lightning has moved northwards of Christchurch... it looks like that band of heavy rain will continue trucking up the east coast making it to around Wellington around the 2-3pm time this afternoon."

The Transport Agency urged motorists in Marlborough, Wellington, Wairarapa and Tararua to drive to the conditions.

Ferris said the risk was mainly for the heavy rain, large hail and strong wind gusts, making driving conditions hazardous.

"That hail [in Canterbury] did really decrease visibility, so if you happen to be out driving out in a severe thunderstorm or a thunderstorm with hail in your path maybe slow down, maybe even pull off the road, it will pass," he said.

MetService warned that large hail, which could come with thunderstorms, could cause significant damage to crops, orchards, vehicles and glasshouses.

Several flights were cancelled and delayed at Christchurch Airport, where MetService said sensors detected 2mm of rain falling in just one minute.

Airways New Zealand said lightning strikes affected some of the "critical infrastructure".

An airport spokesperson said lightning had affected airfield lighting and navigation systems, although the airport stayed open.

The lightning has moved beyond the airport and airport operations are resuming.

Three fire crews were responding to a hedge fire in Yaldhurst sparked by lightning about 10.15am.