Floodwater in Ashburton has become contaminated with sewage after the local wastewater pond treatment facility was flooded.
Ashburton District Council said the situation was now a public health risk and people should avoid all contact with floodwater and assume it is it contaminated.
Those who do come in contact with flood waters should wash affected skin as soon as possible.
People should also change out of any wet clothes and shoes and put them aside to be washed later, the council advised.
Meanwhile, Christchurch City Council also warned that floodwater in parts of Akaroa may also be contaminated.
In a Facebook post this morning, the council said flooding in the tourist hotspot appeared to be caused by blocked pipes.
"The worst of the flooding is around the recreation ground. People should avoid travelling through this area," the council said.
"It is possible the water maybe contaminated. If you do come into contact with flood waters, change out of any wet clothes and shoes and put them aside to be washed later. Wash skin that has come into contact with flood waters, and wash your hands as soon as you reasonably can - or use an alcohol-based hand sanitiser."
Council staff and contractors are on site assessing the situation.
Brittan Terrace and Pigeon Bay Roads are closed due to a slip, and State Highway 75 is now closed at Little River.
Meanwhile, Rue Lavaud, the road into Akaroa township, is currently open with limited access due to severe flooding.
"Please, if you are travelling today, take extreme care on the roads," the council warned.
For continuing live updates on the situation in Canterbury, go here .
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