A state of emergency has been declared in Dunedin and a rain warning for North Otago, Dunedin and coastal Clutha is not due to end until 9pm Friday.
About 100 people were evacuated from homes overnight and evacuation shelters have been opened.
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At least 18 roads were closed across the city due to flooding and slips, with further closures announced in Clutha District.
Another 70 to 100 millimetres is forecast to fall, meaning the region will have received more than two months' worth of rain over three days.
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