Clean-up mode was expected to stall in the eastern Bay of Plenty, which was in for another short deluge of rain overnight as the other end of the country continued to be drenched.
Brief heavy showers were expected to fall east of Opotiki, the MetService said.
Rain caused slips on roads, flooded homes and sparked more than 20 callouts to emergency services in Whakatane.
More than 200mm of intense rain overnight on Monday and yesterday.
A weather analyst called it a "once in a generation deluge" after almost 50mm of rain fell in one hour to midnight.
"That doesn't happen too often at all," said WeatherWatch analyst Richard Green.
Whakatane's War Memorial Hall was open as an evacuation centre for people forced to leave their homes.
Whakatane District Council chief executive Diane Turner said one family was forced to evacuate and others are thought to have left their homes voluntarily.
Rain in the area is expected to ease this morning.
The MetService also said thunderstorms, severe gales and squally showers were possible from Northland to Waikato overnight, and isolated tornadoes were possible in the west of the North Island.
Meanwhile, heavy rain yesterday flooded and almost isolated Oamaru.
State Highway 1 north and south of the North Otago town was impassable, and bypass roads were also flooded.
The Waitaki District emergency management office was activated and motorists were being warned that travel in the area was hazardous.
The Kakanui River breached its banks at several points, as did Island Stream and Oamaru Creek.
A property in York St was evacuated as was the Oamaru Camping Ground, and workers at the Alliance meat works in Pukeuri were sent home at 10am.
Most schools and kindergartens were closed.
In Wellington rain caused flooding on State Highways 1 and 2 in the Tawa, Churton Park and Petone suburbs.
The MetService said it was predicting 80mm to 120mm of rain in the Canterbury foothills and on the hills of North Otago and Dunedin overnight and until this afternoon.
Gales strong enough to damage trees and powerlines and make driving dangerous were also likely on the eastern coast from Kaikoura to Otago and also in parts of Westland and Fiordland. Some were expected to reach up to 130km/h.
Coastal swells of up to 4m at high tide, about 1am, could block off river mouths and flood land.
South Islanders were also warned to brace for snow this week.
Heavy downpours hamper clean-up operation
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