The region was spared further rain as clean-up operations began today, but roads remained closed and water supplies in some areas remained restricted.
Waitaki Civil Defence spokeswoman Rowan Carroll said while it would take some time for all the damage to be assessed, the cost was "definitely going to be in the millions".
"There's just potholes everywhere, sides of roads have been washed out, bridges have been washed away," she told NZPA.
Civil Defence staff were today assessing and prioritising repairs of about 50 rural roads that were closed due to flooding.
"It really will take quite some time and people do have to be very patient," Ms Carroll said.
A New Zealand Army Unimog with two personnel was deployed to deliver food, water and other help to those worst affected.
Police and Civil Defence were also delivering aid and looking for residents who may be isolated because of the high water and land slips.
Some rural water supplies remain restricted to prevent contamination from polluted floodwater, leaving about 1000 residents in Waitaki district without water.
About 3500 people in Palmerston have also had their water supplies disrupted.
The local reservoir has enough water for three days, provided residents conserved water, and the main supply would be restored once the Shag River level dropped.
River levels were falling throughout Otago, but residents were warned to remain vigilant around fast-flowing rivers.
The Taieri River's flow peaked at 1200 cubic metres per second at Outram -- its third highest flow since records began in 1968.
Flood warnings remain in place for the Shag, Waitahuna and Kakanui rivers.
State Highway 1 has reopened between Dunedin and Oamaru but remains closed between Pukeuri and Hilderthorpe, north of Oamaru. A detour is in place via State Highway 83.
Meanwhile, residents of four Napier houses evacuated after a major slip yesterday were allowed to return to their homes about midday today.
One house was still off-limits and its occupants were staying elsewhere.
