"Any thunderstorms that eventuate are expected to produce brief heavy rain of 10 to 20mm per hour, hail of 10 to 20mm diameter and strong wind gusts around 90 km/h," MetService said.
In the lower South Island deep cold air would bring showers laced with small hail to coastal parts of Southland, Clutha and Dunedin, together with a low risk of thunderstorms.
Road snowfall warnings were in place for the Desert Road, SH1, Lewis Pass, SH7, Arthur's Pass, SH73, Porters Pass, SH73, Lindis Pass, SH8 and Crown Range Road until early this morning.
The warning for the Desert Road was in place this afternoon.
Looking ahead to Friday, a narrow ridge over the country would move away to the east allowing a strong and moist northwest flow to spread over central and southern New Zealand.
"An active front is then expected to cross the South Island from the west on Saturday, then across the North Island on Sunday, followed by a change to unsettled westerlies through Monday."
There was a high risk, between Friday and Saturday, that rainfall accumulations would reach warning amounts in Fiordland, the Otago and Canterbury Headwaters, Westland, Buller, and western Nelson.
There was a moderate to low risk for Tararua Range, northern Taranaki and King Country from Saturday to Sunday.
There was also a moderate risk of northwest gales reaching severe gale force around Fiordland, Southland, Southern Lakes, Central Otago, Canterbury and Marlborough, with a high risk about the Marlborough Sounds, Wellington, Wairarapa and the Tararua District during Saturday and early Sunday.
Sunday showed a low risk of severe gales about southern Taranaki, Wanganui, Taihape, Hawkes Bay and Gisborne as the weakening front moved away.
Your weather
Whangārei: Rain this morning, then a few showers until evening. Southwesterlies strengthening this afternoon. High 18C Low 10C
Auckland: Morning rain then showers and hail with possible thunderstorms. Fine this evening. Strong southwest, gusting 100 km/h. High 17C Low 11C
Tauranga: Rain developing morning, hail and possible thunderstorms this afternoon. Becoming fine this evening. Strong southwesterlies. High 18C Low 7C
Whanganui: Rain developing morning, then gradually clearing by evening. Strong southerlies. High 15C Low 7C
Napier: Rain and strong southwesterlies from mid-morning, easing to showers this afternoon. High 17C Low 8C
Wellington: Rain, easing to a few showers this afternoon. Southerlies, strong at times. High 13C Low 8C
Christchurch: Morning showers clearing. Strong southwesterlies gradually easing. High 14C Low 5C
Dunedin: One or two showers. Southwesterlies, strong at times. High 14C Low 7C