Thousands of people around the country are without power, perhaps for 48 hours, and others face a long clean-up after the ex-tropical cyclone.
A State of Emergency was declared for Dunedin to enable evacuations to take place. It followed on from the Buller District, which issued its own early this afternoon.
Dunedin mayor Dave Cull said the city's stormwater system could not cope with the rainfall. The council said up to 800 properties were vulnerable to flooding, mainly in South Dunedin though the number of evacuations needed is not yet clear.
He said sewage had been flowing on the streets in places.
Civil Defence was setting up two evacuation centres. The worst affected areas were Surrey Street in South Dunedin, Kaikorai Valley and Mosgiel.
Late last night, flood waters began to recede around Dunedin but the state of emergency remained in place overnight.
Dunedin City Council said police visited properties affected by wastewater overflows around South Dunedin to check on residents, and give advice to those who don not want to stay in their properties.
Welfare centres in South Dunedin and Mosgiel were closed at 7pm due to lack of demand.
The council said it was not clear how many homes have been affected by floodwaters, but anyone who has been affected should register with the council via its website for follow up as needed.
A number of roads around Dunedin remain closed due to flooding, and some due to concerns about wastewater overflows.
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Elsewhere, residents were being evacuated from low-lying properties in Buller, Nelson and Taranaki, while thousands of properties were without power in Hokitika, Taranaki and Whanganui.
Flights across the country have been affected, with Queenstown and Westport Airports closed.