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A spokesman said a heavy rain warning was also in place for South Westland and inland parts of the lower South Island.
The warning would be in place from noon until midnight today.
"Further showers are expected, which may have a greater than normal impact due to the recent heavy rains.
"These showers may be accompanied by thunderstorms, hail and localised downpours are possible.
"People are advised to stay up to date in case any changes are made."
Otago was hit by more heavy rain yesterday as the recent spell of miserable weather continued.
Between 20mm and 40mm of rain fell in about five hours around parts of Central Otago, North Otago and Dunedin, causing surface flooding and minor damage in some areas.
Many businesses in Gordon Rd, Mosgiel, received minor flooding when drains became inundated by a mid-afternoon downpour.
Aurora Cafe owner Alan Carey said water was flowing in his front door and others along the street.
"It was all over in an hour. By the time we got the sand bags out, it was receding.
"We’ve just got a wee bit of wet carpet and we had to shut a couple of hours early."
Dunedin City Council staff and contractors remain on standby, ready to respond if needed.
Residents concerned about their properties have been urged to sandbag as a precaution.
Sandbag collection sites have been set up again at the Dunedin Ice Stadium, Mosgiel Memorial Park and Strath Taieri Community Hall.
Otago Regional Council duty flood officer Eve Bruhns said she expected the heavy rain to have the most impact on the Manuherikia and Kakanui Rivers.
There were concerns the Manuherikia River could rise significantly, exceeding flows reached over the weekend.
Flows in the Kakanui River were also expected to increase, but remained well under the weekend’s peak flows, she said.
Rivers remained high across much of the rest of Otago, but most had receded and were not expected to rise significantly last night.
Ahead of the expected rainfall, ORC engineering and operations staff and contractors worked at pace, alongside local authorities, to clear debris and blockages, with a focus on Middlemarch and the Maniototo.
At the Taieri River floodbank, near Otokia, the breach was stabilised and monitoring would continue, she said.
"An investigation of the cause of the breach, including hydraulic modelling, is under way to assist with impact assessment and further stabilisation works."
NZ Transport Agency contractors worked overtime to reopen most South Island highways affected by this week’s massive downpours.
NZTA lower South Island transport systems manager Graeme Hall said the only routes which remained closed were State Highway 82, between Kurow and Ikawai, and SH83 between Otematata and Aviemore.
"Work is progressing well at both of these sites, and we’re aiming to have both roads reopened by the weekend.
"The damage on SH83 will require reconstruction of the roadway approaching the Parsons Creek Bridge near Otematata, and while there is some rain in the forecast over the next few days, we’ll be pulling out all the stops to get the job done before the weekend."
Mr Hall reminded drivers speed restrictions remained in place at several sites on the state highway network where flood repairs had been carried out.
On a brighter note, keen cleaners may be able to get some washing dried today and tomorrow morning.
But a MetService spokesman said cold air at upper levels would move on to the South Island tomorrow afternoon, making the atmosphere "unstable" again.
"Heavy showers, thunderstorms, hail and localised downpours are possible in some regions from Thursday to Sunday, especially where winds converge."
He urged residents to keep up-to-date with local forecasts and the thunderstorm outlook in the coming days.