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The Kowhai river breached its banks at 10.26am.
Flooding, slips and road closures could disrupt travel and isolate communities.
Up to 400mm of rain is forecast for northern Canterbury and Marlborough.
Significant rain, strong winds and snow continued in the upper South Island overnight.
Hundreds of Kaikōura households were forced to leave their homes amid flooding.
'Evacuate now. Evacuate to higher ground or inland,' emergency alert says.
Wairoa District Council says floodwaters in the Hawke's Bay town are beginning to recede.