The thunderstorms would be accompanied by a short period of heavy rain, small hail, strong northwest wind gusts, and possibly a small tornado, MetService severe weather forecaster John Crouch said.
"Wind gusts of this strength can cause some structural damage, including to trees and power lines, and may make driving hazardous."
Meanwhile an active cold front is moving northeast over the South Island and lower North Island today bringing heavy rain and strong winds.
The New Zealand Transport Agency has issued two flooding warnings for inland Otago.
The heaviest rain is expected in Fiordland, Westland south of Otira, and the headwaters of the Otago and Canterbury Lakes and Rivers, with 100mm-150mm expected in places.
State Highway 8 from Omarama to Cromwell (Lindis Pass) and State Highway 6 from Cromwell to Makarora are both under caution due to surface flooding "at various locations through this area" today.
Road users were advised to take extra care.
The rain has caused surface flooding in parts of Wanaka. An estimated 21mm of rain has fallen since 6am today and by early afternoon showed no sign of stopping.
Queenstown Lakes District Council said in a Tweet just after 2.30pm it was snowing heavily on the Crown Range Rd and chains needed to be used.
Northwesterly winds are expected to reach severe gale in exposed parts of the Canterbury High Country, Marlborough, Wellington and southern Wairarapa, with gusts up to 130km/h.
Snow is expected to fall to about 400 metres at times over the south of the South Island.
Many alpine roads in the South Island are subject to road snow warnings through to tonight including Lewis Pass (SH7), Arthur's Pass (SH73), Porters Pass (SH73), Lindis Pass (SH8), Crown Range Road, Milford Road (SH94) and Dunedin to Waitati Highway (SH1).
Downer this afternoon said the Milford Road (SH94) would close overnight at 4pm from Hollyford road junction to the chasm due to forecast snow. ]
The road was likely to reopen by 10am tomorrow, but ''significant snow'' was forecast down to low level on Thursday, which could mean an all-day closure.
Over the South Island tomorrow there is a moderate risk of thunderstorms about Kahurangi National Park, Buller and northern Westland through the whole morning, and about Fiordland and Southland before dawn.
These thunderstorms will bring brief heavy rain, hail, and snow to 700-800m in the north of the South Island and to 400-500m about Fiordland and Southland.
Tomorrow afternoon a very unstable west to southwest flow will cover northern and central New Zealand, bringing more heavy showers, thunderstorms and hail.
These thunderstorms are expected to be more frequent about the North Island west coast and Auckland region.
- additional reporting Otago Daily Times
