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Gales look set to hit parts of the Clutha and Dunedin regions during the weekend and early Monday.
The MetService issued a severe weather warning for the regions tonight.
Forecaster Heath Gullery said a strong southwesterly airstream over southern New Zealand would bring a spell of gales and wind gusts could reach 100km/h, possibly more at times, from about dawn tomorrow until dawn Monday, especially near coastal hills and headlands.
Earlier, countless commuters were left stranded after Wellington was blasted by a sudden summer storm.
Trains on the Hutt Valley line have been suspended and some flights in and out of Wellington are reportedly being delayed.
Crews were working on the damage, although it was unknown when the repairs would be completed.
Trees were down across roads, but the only road completely blocked was Paekakariki Hill Road.
The front had moved north this evening, and the weather was expected to improve by overnight.
Tranz Metro is advising passengers to make alternative travel plans after overhead power and signals were damaged by the severe weather.
No cancellations were expected for the Cook Strait ferry, although a tug was being used to manoeuvre the vessels in Wellington harbour as a precaution, an Interislander spokesman said.
Wind gusts of nearly 150km/h were recorded on Mt Kaukau, and the temperature dropped from 19.9 degrees to 9 degrees when the "aggressive" southerly front reached Wellington, weather analyst Philip Duncan said.
Earlier, the wild weather hit Kaikoura, where southerlies gusted to 115km/h and the temperature plunged to 7 degrees.
Karori residents reported seeing hail and flashes of lightning after the storm hit Wellington at about 4.30pm.
Winds were gusting over 120km/h elsewhere in the city. Power lines were down, trees were blown over and there were reports of roofs lifting.
Power lines also came down in Masterton, trapping a car.
Boaties caught out by the sudden storm included a kayaker and several runabouts in Wellington Harbour, Inspector Ian Harris said.
There was also a report of a waka in trouble on Porirua Harbour.
The police launch was called out to rescue the kayaker about 4.30pm near Oriental Bay, and was still searching early this evening, although it was possible the person had made it to safety, Mr Harris said.
Metservice forecaster Chris Noble said winds reached speeds of up to 130 km/h in Kelburn but were now easing off.
Mr Noble predicted a "few more hours of rain" in Wellington but said conditions should clear overnight.
He said an aggressive southerly was slowly travelling up the North Island and was expected to hit the East Coast and Wairarapa regions before reaching Gisborne later tonight.
WeatherWatch.co.nz earlier reported gale force southerlies of up to 115km/h in Kaikoura and a temperature of just 7 degrees, with a drop in temperature of 11 degrees in 35 minutes.
A group of nine American tourists had been reportedly trapped out on a walkway in Kaikoura.
Ward residents reported power outages and Marlborough Lines told Fairfax Media power surges had been reported in Ward, Lake Grassmere, Dashwood and Cloudy Bay Industrial Estate.
Meanwhile, a teenage boy injured after being trapped by a tree branch in Rarangi, near Blenheim, was flown to Wairau Hospital with lower leg and suspected neck or spinal injuries.
In tweets:
amiemccarron: thank you storm for blowing away all the rubbish the dogs spread over yard yesterday - saves me a job :-D
underdog001: just had to run inside as a force of wind came through and forced over half my back fence, branches and fridge sitting outside. #porirua #fb
greeenappple: forget a thunder and lightning storm, we're talking tornado here! epic. unfortunately it has knocked the power out to the fish and chip shop
apanand: Nice cloudy day, driving along, then the sky falls. Windswept furious sheets of rain, tree fragments debris by the road. Indoors time.
mattkward: winds over 130km'h. Hit with this wall of wind and rain, a huge BANG. Car alarms going off. Various objects flying through the air. WOW.
- with NZPA
