Metservice meteorologist Tom Adams said warnings for tornadoes had been in place this evening.
"We have had a lot of severe convection and a lot of thunderstorm on the West Coast and the conditions have been suitable for small tornadoes. Obviously in New Zealand they are not going to be the sort of things you see in America.
"It is not often on the West Coast that you actually get a picture to see that it happened."
He said there had also been very strong winds blowing through Wellington with gusts reaching speeds of up to 140km per hour.
"It is due to peak at 2am overnight but it is not going to get much stronger than that, those gusts may get a bit more frequent. The building is shaking a wee bit," he said.
Mr Adams said the strong winds were ahead of a front which was making its way up the country.
"There are quite a substantial thunderstorms on the West Coast, just north of Westport at the moment as that front is moving north. As that front goes through Wellington overnight.. winds will ease off."
He said gusty winds would continue to make appearances throughout the country next week.
"This pattern is set to repeat to an extent quite a number of times over the next few days maybe not to the extremes we have had this time round but a front moving up and strong northerlies and heavy rain on the West Coast and the Tararuas, we are going to see a bit more of that unfortunately."
The windy weather forced the closure of several of the country's motorways.
The New Zealand Transport Agency advised that the northbound lane on State Highway 1 Kaiapoi to Woodend in the Canterbury region was closed due to fallen trees. SH6 Haast Pass was also closed due to tree debris on the road.
Vehicles were also knocked about by the wind.
On State Highway 73, on the Springfield to West Coast Rd, a trailer overturned while a camper van rolled on SH79, Geraldine to Fairlie.
The Otago Daily Times reported two motorcyclists crashing on the same road due to strong wind gusts.
Surface flooding was hampering drivers on State Highway 6 from Lake Hayes to Queenstown, parts of the Lindis Pass and low-lying side streets in Alexandra, she said.
Airport marketing and communications manager Megan Crawford confirmed flights had been cancelled and delayed.
Airport staff were monitoring the situation, she said.
An Air New Zealand spokeswoman said NZ5053 from Christchurch to Dunedin returned to Christchurch and this caused the cancellation of the return flight while NZ5327 from Wellington to Dunedin returned to Wellington causing the cancellation of that return flight.
Flight NZ5391 from Wellington to Dunedin was diverted to Christchurch, causing the cancellation of that return flight.
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Flight NZ5394 Dunedin to Christchurch had also been delayed, she said.
For up to date flight information, people should check the Air NZ website, the spokeswoman said.
Motorists in the South Island have been warned to take extra care on the roads due to high winds.
Police said there had been two incidents of vehicles rolling, with high winds suspected to be a contributing factor.
A trailer overturned on State Highway 73 on the Springfield to West Coast Road. A recovery vehicle is attending and drivers are advised to avoid the area if possible.
On State Highway 79, on the Geraldine to Fairlie Highway, a campervan rolled.
High winds blew over a caravan on State Highway 85 between Ranfurly and Omakau about 11am.
Nobody was injured, but one lane of the highway was blocked for a short time.
Millers Flat lost electricity about 1.20pm, and it was restored after about an hour and a half.
The road between Arthur's Pass and Springfield was closed due to gusting winds but has reopened.
"We are currently experiencing thunderstorms in Greymouth," West Coast civil defence regional manager Chris Raine said in a warning issued at 3.43pm, that was later lifted.
"Traffic on the road here just piled up - nobody was game to drive on."
Bruce Bay was also hit by a fierce hailstorm this afternoon.
Meanwhile, Mr Raine said yesterday a second bout of rain was expected to hit about midnight with fall amounts of 180mm south of Otira and about 140mm over 12 hours north of Otira on the ranges, with lesser amounts near the coast.
"The hourly rates will increase to 20 to 30mm an hour during squally thunderstorms with damaging wind gusts of 110kph possible and the risk of a small coastal tornado, possibly a waterspout making landfall."
He warned people to stay away from windows in the event of a tornado.
Earlier today, MetService said there was a small chance tornadoes would hit the South Island this afternoon as severe thunderstorms lashed the country.
Many parts of the country could expect wild weather including central and eastern regions.
The storms are expected to bring northwest wind gusts of more than 110km/h and strike southern Westland, Fiordland and Stewart Island.
MetService said there could be one or two small tornadoes in localised coastal areas.
"These squally winds and possible small tornadoes may cause some structural damage, including damage to trees and power lines, and make driving hazardous."
More heavy rain is expected to fall on already deluged western areas of the South Island and Southern Alps.
MetService has issued a warning for the whole of the West Coast with periods of rain expected through to Sunday, while the Westland ranges are forecast to get an additional 180mm of rain today.
MetService warns this amount of rain will cause streams and rivers to rise rapidly and could lead to slips, making conditions dangerous for trampers.
There is also a heavy rain warning for the Tararua Ranges north of Wellington.
The West Coast Civil Defence Emergency Management and Regional Council said it is monitoring all rivers in the West Coast at the moment.
The Waiho River that breached its banks in Franz Josef in March is not causing concern but a stretch of State Highway 67 north of Westport remains closed because of flooding this morning.
The road between Hector and Lamplough has become impassable because of flooding and debris and there are no detours in place.
The New Zealand Transport Agency is also cautioning drivers using the highway north of Westport to Mokihinui to beware of surface flooding.
