About 40 roads in North Otago are closed as the South Island's east coast mops up from a midwinter deluge.
The New Zealand Transport Agency is warning motorists of flooding on a number of state highways in the South Island and roads around Dunedin were closed on Wednesday.
The Oamaru-based Waitaki District Council is urging people in rural areas to stay home.
Major rivers in the district are peaking and the smaller rivers struggle to cope with the massive amount of water that has fallen on the district.
The district was "100 per cent saturated" and 20mm of rain ran off the land, council emergency services manager Chris Raine told NZ Newswire.
"The heavy rain is certainly over, the problem is the catchments are full of water.
"We can't guarantee the road people go to town on will still be open when they want to go home."
The Kakanui River had broken its banks at Maheno and flooded the bowling club, but that was the only report of property damage.
Three significant rainfalls in two weeks was a bit unusual and a "phenomenal" amount of water was flowing from the catchments out to sea, Mr Raine said.
Meanwhile, in Christchurch, as a precaution authorities advised people in three houses in the Port Hills suburb of Hillsborough to leave on Tuesday because heavy rain was forecast.
However, the Fire Service and Christchurch City Council on Wednesday morning said no major flooding was reported overnight.
The Metservice says rain should clear on Wednesday morning in Canterbury and Otago.