A state of emergency has been declared in Southland as extensive flooding causes significant problems across the region.

Southland Civil Defence Emergency Management Group chair Neville Cook declared the state of emergency for the region on Tuesday afternoon, including Gore, following Monday's declaration for Milford Sound, where 195 tourists remained trapped. 

Rivers were continuing to rise, many roads were closed and landslips were occurring throughout the region after torrential rain has battered down for three days.

The Gore District Council was advising motorists not to travel unless it was absolutely necessary.

Council deputy chief executive Ian Davidson-Watts said flooding was threatening some homes in Gore.

"We have staff going door-to-door in the worse affected areas to talk with residents and ensure they are okay."

Some properties have been sandbagged, and flooding waters had entered several basements and garages.

The council was also keeping a close eye on the Otama Water Supply pipeline, which crosses the Mataura River at Pyramid.

A council spokeswoman said it was a concern, but there wasn't much the council could do, and there were contingency plans in place should the line go.

The scheme supplies water to 200 rural properties.

Advance Agriculture staff took 600 seed bags from its Invercargill branch and to Allied Concrete in Gore to assist with making sandbags and would provide another 1000 if needed. 

Several state highways in the area are closed: SH1 Gore to Clinton, SH1 Mataura to Gore, SH90 McNab to Tapanui, from SH1 intersection to Station Rd, SH90 between SH1 and Station Rd. SH97 Mossburn to SH6 intersection SH97 is CLOSED. State Highway 94 is closed from Park Boundary and SH96 from Lumsden to Frankton. 

Flooding in the district and in West Otago had forced 17 schools and two early childhood centres to close. The closures affected 1877 school students and 70 children in early learning.

Gore district mayor Tracy Hicks said he had seen the Mataura River, which flows through the Gore and Mataura townships, higher than it was flowing on Tuesday, but he had never seen so much floodwater lying around.

The floodwaters had "really started to show its head yesterday" and the council and fire service had begun pumping water away to protect properties and buildings.

Southland Federated Farmers vice president Bernadette Hunt said she had not heard of any catastrophic damage in the region, but farmer's fences and culverts could be damaged.

"We'll all cope, as long as a floodbank doesn't burst or something like that."

Beef + Lamb New Zealand urged farmers in the region to move their stock to higher ground.

Company Southern South Island extension manager Olivia Ross said "where it is safe to do so, farmers are encouraged to check their stock and move them to high ground and move baleage to ensure it is not carted down swollen rivers."

Precautionary measures were being taken to protect a hazardous substance being stored in a building in Mataura, which gives off ammonia gas if it gets wet.

About 10,000 tonnes of ouvea premix, a class six hazardous substance, was being stored in the former paper mill in the township, which is right next to the Mataura River. 

On Tuesday afternoon the Mataura River at Gore was flowing at 2.7m above normal.

Mataura resident Dave Mackenzie said he was nervous about the presence of the ouvea premix and what could happen if the river continued to rise.

"Once it's mixed with water it causes a gas eruption. This is the highest I've seen the river in the 12 years I've lived here. 

"I guarantee people are worried [about the river and premix]."

However, Mataura Community Board chairperson Alan Taylor was comfortable that the situation was under control.

"We have heard the company that is responsible for that is looking after that. The [Gore] District Council has been in touch with them to make sure they are doing their job and making things secure there."

Gore District Council chief executive Steve Parry said he had asked Inalco, the company that was moving the premix from the building, to take precautions to protect it, in case flood waters continued to rise.

The company had stopped its operations removing the substance from the building on Tuesday morning.

He had also been liaising with Emergency Management Southland about the issue.

"I'm as concerned as anyone else about the infiltration of the river into that building, as that would be catastrophic."

Regional Ford salesman Robin South said he hadn't seen constant rain and flooding in Gore for a long time.

"It's been too much for the town's drains."

A few of the company's customers, visiting from Invercargill on Tuesday, had to detour around closed roads at Mataura, South added.

"The [nearby Mataura] river is definitely rising, by crikey it is."

An Emergency Management Southland spokesperson said Environment Southland hydrologists were currently assessing river levels in the province.

Clutha River at Balclutha is expected to rise to 2200 cumecs between 6 and 11pm on Tuesday night before climbing to 2500 cumecs by 4.00am Wednesday morning.

River levels this high will make the Owaka Highway outside Balclutha impassable.

Clutha District Council has made the decision to close the road to all traffic at 5.30pm on Tuesday.

Welfare Centres will be opened at that time at the Cross Recreation Centre in Glasgow St, Balclutha and at the Owaka Community Centre.

A community hub has also been set up at the Lumsden Community Hall for support and advice for anybody caught up in the flooding.