Lewers issued the state of emergency on Friday, following a similar declaration in the nearby town of Gore, and in Southland on Thursday.

Gore received 102mm of rain overnight, with dozens of volunteer firefighters and locals called in to place sandbags to save properties from flooding.

Mt Cook Village received 120mm in an unseasonably hefty dump.

The downpour was expected to ease later on Friday. Forecaster Metservice issued warnings for snow to low altitudes across Otago and the Canterbury Plains.

A number of highways in the region are closed, though the road to Milford Sound which received 318mm on Thursday, has reopened.

While no injuries have been reported, further damage could follow.

Rivers in the region, including the Mataura River - a legendary waterway for brown trout fishing - were expected to peak later on Friday.

The nearby Waikaia River has burst its banks, affecting farmland.

The flooding and landslips follow an outbreak of the parasite cryptosporidium in Queenstown.

At least 18 cases of the highly infectious bug have been identified this week after complaints of stomach cramps and diarrhoea. Social media posts suggest a more widespread problem.

While the origin of the outbreak is yet to be confirmed, public health authorities have issued a boil water notice as a precaution.

The national water regulator has issued a compliance order on Queenstown Lakes Council’s Two Mile treatment plant for not having an appropriate parasite filter.

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Lewers said a fix that could prompt the regulator to lift the boil water notice was still a way off.

“A best case [scenario] would be months ... to get the kit to here and install it, it could take some time,” he said.

“We have to take a risk management approach.”

Radio NZ reported local businesses were resorting to bringing in water from nearby lakes to keep their coffee machines running.