People in these areas should be on the lookout for threatening weather conditions, they said.
Metservice said Lindis Pass and Crown Range Rd could expect snow showers overnight.
The snow is predicted to turn to rain about noon tomorrow at Lindis Pass, and during this period, a further 2-5cm could accumulate near the summit.
The thunderstorm warning follows a day of rainy and windy weather that battered Auckland, with windows blown out at a central city hotel and a number of roads flooded.
Piha faced the most rain, with 80.5mm rain over 18 hours.
Emergency services were at Piha Domain Motor Camp where people were wading through knee-deep water.
The country is set for grim weather this weekend as persistent rain settles in.
Metservice meteorologist Doug Mason said a low pressure system and an associated front moving across the Tasman Sea is bringing the unsettled weather.
But despite the wind and rain, temperatures won't be cold on Sunday, thanks to a warm northeasterly flow with most of the North Island expecting highs of between 20 and 25 degrees.
Around Southland and Central Otago will be chilly tomorrow, with temperatures predicted to drop to 2 degrees overnight in Invercargill and 8 degrees in Queenstown.
