About 130 homes in the flooded Henley and Taieri areas near Dunedin remain empty for another night.
"Some of these residents may not be able to return to their homes for several days," says Dunedin civil defence controller Sue Bidrose.
Fine weather on Sunday allowed councils in Otago and Canterbury to clear slips and open many roads after a winter storm dumped record amounts of rain.
The weather station at Oamaru Airport had 147mm of rainfall, more than triple the July average of 40mm, says MetService meteorologist Angus Hines.
People are being warned flood water is likely to be contaminated, farmers are making arrangements for stock, and slips are being cleared from roads. Welfare centres have closed.
There was some fresh flooding on the roads around the lower reaches of the Heathcote River at high tide on Sunday evening but this was expected to subside quite quickly as the tide went out, Christchurch City Council said.
MetService said the rain storm was so devastating because it was slow moving.
Most places from Christchurch to Dunedin recorded more than the long-term average July rainfall in just 24 to 48 hours.
A state of emergency was called in many South Island towns and the army sent in troops and trucks.
A pair of fronts are due in the next few days but the heaviest rain will be in western areas of the South Island.
A heavy rain warning is in place for a burst of heavy rain in Fiordland early on Monday morning, while a severe weather watch for heavy rain has been issued further up the west coast.
From Thursday, another winter storm with rain looks likely to affect Canterbury and much of the South Island.
Civil Defence Minister Nathan Guy said civil defence emergency management groups had acted proactively and decisively to keep people and property out of harm's way.
"The impacts of these floods will be felt for some time in communities throughout Canterbury and Otago. The Government is ready to provide support where it's needed, and financial assistance is available to local authorities that have been affected," he said.
While local states of emergencies were being withdrawn as river levels in both Canterbury and Otago receded, authorities were mindful further rain was forecast in coming days, he said.