Westland, Buller and northwest Nelson were under heavy rain watches, with up to 80mm of rain expected by this evening.
The was also a moderate risk of thunderstorms through these areas in the afternoon and early evening, and over Taranaki and Waitomo at night.
These thunderstorms could produce heavy rain of 10 to 20mm per hour, small hail, and for Taranaki and Waitomo possible strong wind gusts of 90km/h.
There was also a risk of thunderstorms across the lower South Island in the afternoon and evening, due to unstable northwesterlies.
Tomorrow these fronts would clear the country, ahead of a southerly change on Friday pushing another bout of rain up the South Island.
That southerly change would bring rain to parts of the lower North Island and to Taranaki early Saturday.
By the time it reached Auckland in the evening it would have weakened, and fully cleared the island overnight leaving a ridge of high pressure.
"Sunday will be the day of the weekend across the country," Miller said.
The ridge would move slowly east on Sunday as a complex trough approached the South Island from the Tasman Sea.
The trough was expected to move over New Zealand on Monday, bringing rain to the western and northern areas of the country, and preceded by strong northwesterlies.
Today's weather
Whangārei
Mainly fine, chance evening shower. Westerly winds. 18C high, 12C overnight.
Auckland
Partly cloudy. A few showers, mainly this evening. Westerly winds. 17C high, 12C overnight.
Hamilton
Cloudy at times. Showers developing this afternoon. Northwest winds. 16C high, 10C overnight.
Tauranga
Fine, then a few showers at night. Westerlies. 17C high, 11C overnight.
New Plymouth Becoming cloudy. Showers developing this afternoon, frequent this evening and possible thunderstorms. Northwesterlies. 15C high, 11C overnight.
Napier Fine. High cloud by evening. Northwesterlies developing afternoon. 18C high, 11C overnight.
Wellington Becoming cloudy. Showers developing afternoon, chance heavy from evening. Northerly becoming strong this afternoon. 14C high, 11C overnight.
Nelson Becoming cloudy. Some rain from afternoon. Northerlies from late morning. 15C high, 5C overnight.
Christchurch High cloud. Northeasterlies, dying out this evening. 16C high, 4C overnight.
Dunedin Cloudy periods. Some light rain this morning. Northeast, dying out this afternoon. 16C high, 5C overnight.