Meanwhile, western parts of the North Island were "not looking too bad", Loots said.
Auckland was in for a day of fine spells and a high of 25C. Similar conditions were forecast for much of the upper North Island.
Much of the South Island was also in for a fine summer's day.
It is a different story for the North Island's east coast however, with a heavy rain warning in place since 9pm last night and lasting until 9pm tonight for part's of Hawke's Bay.
About 100 to 120mm of rain was forecast in the Wairoa District, and elsewhere in the hills and ranges.
Loots said overnight some parts of Hawke's Bay had seen 20-30mm of rain, but this would ramp up through the morning and hit Gisborne this afternoon and evening.
There was also a moderate risk of thunderstorms from central Hawke's Bay to Gisborne today, with potential for heavy rain up to 25mm per hour and small hail.
In the afternoon there was a moderate risk of thunderstorms also for Waikato, Waitomo, southern Coromandel Peninsula and Bay of Plenty, with potential for heavy rain and hail.
The low affecting the North Island should move away to the east on Thursday while a weak trough moved on to the south of the South Island from the southwest.
A ridge should then cover much of New Zealand on Friday bringing a return of fine weather.
Today's weather
Whangārei Fine spells. Southwesterlies. 26C high, 18C overnight.
Auckland Fine spells. Possible shower early and late. Fresh southwesterlies. 25C high, 18C overnight.
Hamilton Fine spells. A few afternoon showers, chance heavy. Southerlies. 26C high, 14C overnight.
Tauranga Morning rain, then showers, possibly heavy. Southwesterlies. 25C high, 17C overnight.
New Plymouth Fine spells. Fresh southerlies. 24C high, 13C overnight.
Napier Rain, heavy at times and possibly thundery. Southerlies. 22C high, 17C overnight.
Whanganui Fine spells. Southerlies dying out. 23C high, 14C overnight.
Wellington Mostly cloudy. Southerlies gradually dying out. 19C high, 13C overnight.
Nelson Fine. Light winds and afternoon sea breezes. 23C high, 14C overnight.
Christchurch Becoming fine early morning. Northeasterly developing afternoon, and dying out evening. 20C high, 13C overnight.
Dunedin Fine, but some evening cloud. Northeast dying out evening. 23C high, 15C overnight.
