Flooding has closed roads and threatened properties around Porirua, while heavy snow has blocked roads in the South Island.
There had been 21,500 lightning strikes over land and water in 12 hours, with more thunderstorms predicted for large swathes of the country, MetService said.
Heavy rain has kept emergency services busy around Porirua, with firefighters attending 7-8 jobs since midday where water was threatening people's houses.
FENZ central shift manager Karen McDonald said the water had not got inside most houses but was threatening to.
As well as road closures there were a number of hazards on the road. Firefighters had not been called to deal with any fallen trees in the area.
Porirua mayor Anita Baker told RNZ floodwaters were rising around some houses in Mana and Plimmerton and more torrential rain meant things were expected to get worse. Firefighters were trying to pump the water away.
"It's gone into their garages - I've got a lady who's keeping in constant contact - it's already in their garages, but their house is a little bit higher, but it's surrounding their houses and their heat pumps and things like that, so it can't be far away."
Waka Kotahi NZTA Wellington said a slip had closed State Highway 58 between Oak Ave and Postgate Dr, and SH59 from Mana View Rd to Acheron Rd was closed by flooding.
Surface flooding was also affecting the state highway network across the region, which is under a heavy rain warning.
MetService said there was also flooding in Whitby in Porirua due to overwhelmed drains.
Meanwhile in Whitby, north Wellington, heavy rain downpours from passing thunderstorms are overwhelming drains & causing flooding. Don't drive through floodwaters as you could get stuck! The MetService radar is great for tracking the heaviest rain https://t.co/lbZO6L78FY ^LM pic.twitter.com/JoSsPgIJHT
— MetService (@MetService) June 12, 2022
Forecasters have warned people to "batten down the hatches" with severe weather watches and warnings in place across the country.
Those in the firing line of wind warnings should secure trampolines and remove other loose items that could be turned into "missiles" as strong winds approach.
They should get ready for possible power outages and check on pets and neighbours.
Fresh severe thunderstorm watches have been issued and now include Auckland, Northland, Waikato, Waitomo, Taranaki, Kapiti-Horowhenua, Wellington, Marlborough, Nelson, Buller, Westland, Canterbury High Country and Fiordland.
In those areas, frequent thunderstorms are forecast to bring heavy rain, hail, strong squally wind gusts, and possibly some small tornadoes about coastal areas, MetService says.
The Severe Thunderstorm Watch has been updated. Valid until 6am Monday. These thunderstorms are forecast to bring heavy rain, hail, strong squally wind gusts, and possibly some small tornadoes about coastal areas. More details here https://t.co/qHyE5zzql5 pic.twitter.com/2PVZC6MuK7
— MetService (@MetService) June 11, 2022
The watches are in place until 6am Monday and thunderstorms could become severe - bringing large hail, damaging winds and "possible one or two damaging tornadoes near the coast".
Wind gusts could cause structural damage including to trees and power lines, and could make driving hazardous.
MetService meteorologist Stephen Glassey said for Auckland, Northland and Waikato the main thunderstorm risk would be overnight.
"It's very stormy weather across many parts of the country ... as well as squally thundery showers, there's also strong winds and heavy rain."
The weather system was sitting in the Tasman Sea but had come up from the south and had brought a lot of cold air with it. Eastern areas that were more sheltered were not getting such bad weather, Glassey said.
Strong wind warnings were in place for Wellington and southern Wairarapa, Marlborough, the Canterbury High Country, Westland and Buller. Gusts of 120-130km/h were expected, he said.
For those areas under thunderstorm watches, there was a risk of gusts over 110km/h even if they weren't covered by a wind warning.
The Tararua Ranges and Westland are under heavy rain warnings until midday Monday, with 110 to 150mm of rain expected.
Kapiti-Horowhenua, Tararua, Wairarapa, Wellington, Westland are also under heavy rain warnings and many other areas are under heavy rain watches.
Heavy rain has also been hitting Auckland overnight. This morning, MetService warned thunderstorms would arrive in the city before midday but the storms have now weakened and are likely to arrive south of Auckland.
Heads up Auckland! There is a line of thunderstorms moving towards you from the west. Due in the next couple of hours. Check the Auckland radar here https://t.co/7k3nmeeZKF pic.twitter.com/4oFzLdSNrc
— MetService (@MetService) June 11, 2022
It's still snowing in the lower South Island, though not as low as Saturday when snow was down to sea level, Glassey said.
Road snowfall warnings have been issued for the Desert Rd, Lewis Pass, Arthur's Pass, Lindis Pass, Crown Range Rd and Milford Rd.
Waka Kotahi NZ Transport Agency said Lindis Pass was closed just after 10am because of heavy snow, while snow had also closed Milford Rd and Crown Range Rd.
SH8 TARRAS TO OMARAMA, OTAGO - SNOW - 10:20AM
— Waka Kotahi NZTA Otago & Southland (@WakaKotahiOS) June 11, 2022
Due to heavy snow, the road is now CLOSED at Lindis Pass. Please avoid this area and delay your journey if possible. An update will be provided when the road status has changed. ^FP pic.twitter.com/SYJ78ZOwR1
Snow blanketed parts of Central Otago yesterday and wild weather again left a trail of destruction in the Horowhenua District.
The South Island will continue to bear the brunt of the extreme weather today, where 11 warnings or watches are in place.
MetService meteorologist Gerard Bellam earlier said a deep low was crossing the country, with warnings of heavy rain, severe gales, snow and large swells in various areas.
"So it's sort of a day to think about putting off travel and battening down the hatches."
"Frequent thunderstorms are expected about western and northern parts of New Zealand from the early hours of Sunday morning," MetService said.
"These thunderstorms are forecast to bring heavy rain, hail, strong squally wind gusts, and possibly some small tornadoes about coastal areas."
Bellam told the Herald the whole country should keep up to date with forecasts, warnings and watches as the weather was affecting large parts of the country.
"Especially in the South Island, we have a lot of road snow warnings out across most of those higher road passes."
MetService has put strong wind warnings in place for Buller, Canterbury High Country, Marlborough, Wairarapa, Wellington and Westland, while many other areas are under a strong wind watch.
Buller and Westland emergency management this morning warned locals to turn trampolines upside down and bring anything loose indoors, warning "branches and firewood can become missiles in strong winds".
"Bring pets indoors. They can get unsettled by thunderstorms and it is more comforting and safer for them to be with you."
People should also check on their neighbours, be careful driving and be cautious around coastal areas as seas could be hazardous.
Further south, a heavy rain warning is in place in Westland south of Otira until Monday 9am and there is a road snowfall warning ending this morning for Arthurs Pass, and the Milford Rd until 11pm. Snowfall has closed Milford Rd until further notice.
UPDATE 8:30AM, SUN 12 JUN
— Waka Kotahi NZTA Otago & Southland (@WakaKotahiOS) June 11, 2022
SH94 Milford Rd will remain CLOSED, due to continuing snowfall. Please continue to avoid the area, the next update is on Mon 13 Jun morning or earlier if conditions change. ^FP https://t.co/1WtVFwqesA
Horowhenua was hit particularly hard yesterday by heavy rain as well as reports of a tornado by one family.
Horowhenua mayor Bernie Wanden told residents yesterday while they had been able to manage most of the flooding in town, a few houses were damaged.
"And we're looking to find some accommodation for a few people overnight."
Wanden said the area's water treatment plant could not handle the volume of muddy water so it was unable to operate to its capacity.
He urged residents to conserve water and only use it for essential purposes for the next few days.
"Please if you can, just stop using water unless you absolutely need to and also if you don't need to go out please stay home."
Ōhau resident Kim Udy told the Herald they were in bed about 11.30pm Friday when a tornado hit their property.
"It lasted 30 seconds but that 30 seconds was absolutely terrifying to say the least."
Udy told the Herald they are in the process of building so are living in a caravan, and her husband had built what he thought was a solid shelter coming off the caravan.
However, the weather was too wild, and Udy said the structure, along with the trampoline they got for their daughter, had been destroyed.
"I'm pretty certain it moved our caravan, which is 26 foot."
The couple's chicken coop had been "absolutely" ruined, but the birds were fine.
"I'm currently staying at my sister's house in Levin with my daughter; I'm a bit too scared to go back home in fear that it will happen again."
It's not all bad weather news as Cardrona ski field opened early and other ski fields down south are set to follow suit in the coming days.
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