Up to 120mm of rain was expected in the ranges and coastal hills, and up to 80mm elsewhere in the next 24 hours.
Thunderstorms were also possible this morning.
"There is a moderate risk of thunderstorms for Hawke's Bay north of Waipukurau, and a low risk in a slightly broader area that includes the remainder of Hawke's Bay plus Gisborne south of Poverty Bay," MetService said.
A warning was also in place for the Wairoa District with 70mm about the ranges and 50mm elsewhere.
A heavy rain watch was in place for the Tararua District with expected periods of heavy rain, especially in the north.
A strong wind watch was in place for Taranaki with southeast winds expected to approach "severe gales" at times.
Up north Auckland would again get spells of showers in the morning but that should clear by evening.
In the South Island fine conditions were forecast across the board with some cloud coverage about Nelson and Blenheim in the afternoon.
Looking ahead, a cold and moist south to southeast flow affects the North Island through to early Sunday.
"There is moderate confidence of rainfall reaching warning amounts over the ranges and coastal hills of Hawke's Bay and Gisborne during Thursday and Friday, while confidence is low over the Wairarapa during this time.
"South to southeasterly gales are likely to affect exposed southern and western parts of the North Island, and there is low confidence of these gales becoming severe in exposed parts of the Island from Taranaki to Wellington during Thursday."
In the south, a ridge of high pressure would move slowly across the South Island from Thursday to Saturday, with frosts likely in sheltered places.
Today's weather
Whangārei: Cloudy periods, chance shower from afternoon. Southerlies. High 15C Low 6C
Auckland: Fine spells. However, isolated showers from late morning, clearing by evening. Southerlies. High 15C Low 7C
Tauranga: Cloudy periods with the odd shower, especially in the evening. Southerlies. High 15C Low 6C
New Plymouth: Cloudy periods, chance shower. Strong southeasterlies. High 12C Low 8C
Napier: Rain, with heavy falls and chance thunderstorms in the morning, easing overnight. Strong gusty southerly, easing evening. High 14C Low 8C
Wellington: Periods of rain. Southerlies, strong in exposed places. High 10C Low 8C
Christchurch: Cloudy periods. Easterly breezes. High 10C Low 3C
Dunedin: Fine, apart from evening cloud. Northeasterly. High 11C Low 5C