Residents in low-lying areas of Gore, Wyndham, and Mataura were evacuated as the flood emergency continued.
Riversdale residents were also asked to prepare to evacuate if necessary.
A toxic gas could be released if the Mataura River floods and water seeps into an old paper mill.
The area has been hit by severe rain and the river has now breached at high tide.
What you need to know:
- State of emergencies are in place for Southland, Fiordland, and Clutha
- About 6000 people have been evacuated or are preparing to be evacuated throughout Southland and Fiordland
- A toxic ammonia gas could be released if water from the Mataura River overflows into an old paper mill
- People are being told to treat all flood waters as contaminated and stay away
- Power has been cut to flood zones in Gore and parts of Mataura
- People are being urged to conserve water
- Schools in Gore are closed on Wednesday
- Community hubs have been set up at Calvin Community Church, and Croydon Lodge. People can evacuate with pets to Waimumu Hall.
These live updates have now finished.
7:13pm - State Highway 6 just north of Invercargill has reopened for heavy vehicles, as has State Highway 96 between Winton and Mataura.
6:01pm - Here's a map of current road closures issued by NZTA.
A live map with more details can be viewed here.
5:41pm - Winton's Presbyterian Church - 30km north of Invercargill - has opened its doors to those stuck in the town for "tea, coffee and advice" while State Highway 6 to Invercargill remains closed.
5:35pm - Minister of Rural Communities Damien O'Connor is in Southland.
A Twitter post from him says the floods have put immense pressure on farmers, to the point where they're beyond their ability to cope.
"I have declared an adverse event for the Southland and Otago regions," the tweet says.
"This unlocks extra funding of $100,000 for the Rural Support Trusts to help speed up the recovery."
5:28pm - Gore residents will be able to return home from 6pm.
Emergency Management Southland says the Mataura River has receeded enough since it peaked at midday that they're "confident" people can go home.
"We've been encouraged by the reducing water flows in the river, and latest projections show that the river flow should be back down to around 2000 cumecs by 6pm, which is well below the design level for the flood bank," Civil Defence controller Ian Davidson-Watts says.
"We thank people again for the way they responded when we needed to evacuate at short notice, and appreciate their patience while they have been away from home."
The Gore bridge has reopened to traffic, which opens up access to and from Clinton via State Highway 1.
State Highway 1 is still closed at Mataura, and the town is still evacuated.
5:18pm - Emergency accommodation is being offered in Invercargill to anyone who requires it.
People who are stuck due to road closures and flooding can head to either Murihiku Marae on Tramway Rd or Nga Hau E Wha on Conon St.
5:09pm - All highways in and out of Invercargill are closed.
The Highways South Facebook page says State Highway 99 at Wallacetown is closed as well as State Highway 6 at Ryal Bush due to flooding at their respective Makarewa River bridges.
4:32pm - Airbnb has opened its Open Homes Program, which enables hosts to list their homes free of charge for emergency accommodation.
Airbnb's country manager Susan Wheeldon is encouraging those living near affected areas to open their homes to impacted residents and emergency workers.
"Airbnb's Open Homes Program helps connect both residents in need of housing and emergency workers with free temporary accommodation," she said in a statement.
"We are very grateful to those hosts and residents who have already opened their homes to provide free housing and we encourage anyone living near affected areas to consider doing the same, if they are in a position to assist."
The program is available until February 18 and can be accessed here.
4:26pm - A convoy is due to depart from Te Anau at the Five Rivers Junction and Frankton each hour until 7pm tonight.
The convoy will depart from the Five Rivers Junction - the intersection of State Highways 6 and 97 - which began at 4pm this afternoon. It will then leave at 5pm, 6pm and 7pm.
NZTA is organising the convoys, and it will take traffic through to Frankton, near Queenstown.
As one convoy leaves from Frankton's Lakeside Estate - where the highway closure is in place - and heads south, the other will depart from Five Rivers and drive north. The route is about one hour long.
Drivers leaving Te Anau will detour around The Key area and drive through to Five Rivers via State Highway 97. Once they arrive at Five Rivers, they will join the convoy queue.
Access south of the Five Rivers intersection towards Invercargill is unavailable due to the Makarewa River levels closing two key bridges.
4:05pm - Photos supplied to Newshub show how rising water is impacting locals and their properties.
3:36pm - The New Zealand Defence Force (NZDF) has sent a helicopter, two Unimog vehicles and personnel to help evacuate people trapped by flooding, it confirmed in a statement.
A Royal New Zealand Air Force (RNZAF) helicopter left RNZAF Base Ohakea - near Palmerston North - for Invercargill this morning. It will carry out flights to assess damage and assist evacuations near Mataura, Gore and Wyndham.
Two New Zealand Army Unimog trucks - each with four soldiers - are in Mataura this afternoon. They will also help evacuate people.
NZDF liaison officers are working with Emergency Management Southland to coordinate tasks and resources.
3:19pm - If a house is damaged by flooding, Southland electricity supply company PowerNet recommends a registered electrician inspects the property before power is restored.
Power will only be restored if an electrical certification document is shown.
3:11pm - Southland Civil Defence controller Angus McKay released a statement to ease fears about the potential release of ammonia from the Mataura paper mill.
"We've addressed the situation to the best of our ability. We have a very large cordon around the paper mill due to the flooding.
"We are aware of the potential risks of the ouvea premix. We've got a wide evacuation zone around the area. The risks associated with the premix have been considered when setting the evacuation zones around the paper mill.
"There's so much water going down the river that any contaminants that leach into the river will be diluted."
The area is still evacuated and they have had no reports of any ammonia coming from the paper mill yet.
3:02pm - Minister of Civil Defence Peeni Henare says he will arrive in Southland tomorrow.
He told reporters that the Government is on "high alert" with the situation.
"We've been in contact with the local mayors. They're happy with their control at the moment, but of course we look to the gods and hope we don't get anymore rain there."
Watch the full video here.
2:35pm - Invercargill City Council Councillor Toni Biddle is advising anyone travelling from Dunedin to Invercargill after the Elton John concert to stay put.
"The concern is not the road as it is now but when the [Mataura] river reaches peak and the result of the flood waters at that time. The river is expected to peak this afternoon."
Emergency Management Southland is also urging people to stay in Dunedin.
"We cannot emphasize this enough - if you are in Dunedin, or between Dunedin and Invercargill, and are intending to return to Invercargill - please do not attempt this. Stay put, stay safe," it wrote on Facebook.
2:19pm - A toxic ammonia gas may be released in Mataura from an old paper mill.
The mill is in the flood zone and houses ouvea - a substance that, when mixed with water, creates the toxic gas.
If the Mataura River overflows and water seeps into the building, the surrounding area will need to be evacuated and all exposed people will need medical attention.
The material is stored in large, extra lined plastic bags.
2:11pm - The Mataura River is expected to remain "consistently high" for several hours, Emergency Management Southland said on Facebook.
1:58pm - A road near Gore has been torn up by flooding.
1:27pm - More than 100 dairy farms in Southland and south Otago are being severely impacted by the extensive flooding in the region, according to DairyNZ.
Read more here.
1:23pm - The behaviour of motorists trying to get through flooded areas is causing concern.
People trying to back to Southland from Dunedin following Tuesday night's Elton John concert are finding they can't.
"There is no way through, roads are closed," Emergency Management Southland said on Facebook.
"Please do not attempt these roads as you will not get through."
1:02pm - DairyNZ South Island manager Tony Finch says it's a dire situation for many farms.
"The flooding has impacted effluenet management systems on many of the farms so farmers now also face the challenge of how to dispose of this in the best way.
"Any farmers needing advice on managing effluent should get in touch with their local councils."
12:57pm - Motorists in Southland are being asked by police to avoid all non-urgent travel.
12:42pm - A large chunk of low-lying Gore has been evacuated as the flooding emergency continues.
About 220 people have gone to the main emergency hub - Calvin Community Church, Minister Ken Williams told Newshub.
12:25pm - The Insurance Council says the impact of the flooding for home owners and business is not yet known.
12:07pm - Otago travellers are being asked not to drive south until the state highways have reopened.
State Highway 1 is closed between Clinton and Gore, while SH6 between Frankton and Lumsden is also closed.
Local roads in all the areas are also affected so there are no detours.
11:57am - In Dunedin, beachgoers are being warned to stay out of the water for 48 hours after partially treated wastewater was discharged into the sea.
Some roads will remain closed for most of the day.
11:44am - Dylan McCleary farms near Mataura and his family self-evacuated on Tuesday night.
He's now helping friends move stock feed from flooded sheds beside the fast-running Mataura River.
"Hopefully everything will be fine," he says.
11:39am - Fonterra regional head of Southland and Otago Mark Robinson says the company will be working with farmers impacted by the flooding.
"Our focus is on making sure our farmers and employees affected by the flooding are safe," he told Newshub.
"Milk collection has been disrupted with a number of road closures and flooded access ways.
"Many farms are flooded - so [it's] obviously a stressful time for farmers."
11:33am - Emergency services have been sandbagging a building on the banks of the Mataura River to protect potentially hazardous material from floodwaters.
11:29am - A video of some of the inundation shared to Facebook by local National MP Hamish Walker on Wednesday morning shows the extent of the devastating flooding in the area.
Watch the video above.
11:14am - Clutha-Southland MP Hamish Walker says it's a increasingly difficult and dangerous situation.
"I will be providing regular updates on my Facebook page and I encourage people to keep an eye on advice being circulated by Civil Defence Southland."
11:03am - Authorities are concerned about potentially hazardous material stored on the banks of the Mataura River ahead of its peak.
It's in the Mataura paper mill and comes from the aluminium process at Tiwai.
Emergency Management Southland says it's yet to determine what the environmental impact could be if it comes in contact with floodwaters and the building is being sandbagged.
Gore District Mayor Tracy Hicks says it's not easy to move out.
"The company that put it in there went into liquidation so there's a combine effort of the council, [and] the Government - to move it," he told Newshub.
10:41am - South Gore has become inundated and power is being cut to flood zones for safety.
The river is set to peak at Mataura within the next half hour.
10:40am - In Fiordland, the evacuation of 195 tourists from cut-off Milford Sound got underway at first light.
Helicopters are flying them to Knobs Flat where buses are waiting.
The Milford Rd repair is expected to continue well into next week.
10:33am - Motorists are being urged to take extra care in the Southland region due to the flooding.
"Some roads are closed and may remain closed into the weekend," police said in a statement.
9:59am - Newshub's Dave Gooselink says residents have received automated alerts from Civil Defence via text message people to evacuate.
9:54am - Local authority PowerNet says power supplies have been disconnected due to public safety concerns.
Power has been cut to flood zones in Gore and parts of Mataura.
"We will notify the affected areas on our outages website as well as through our Facebook page," PowerNet chief operating officer Justin Peterson said.
"The safety and well-being of employees and the community are our first priorities when working in a state of emergency."
9:52am - The river is expected to peak at Mataura in less than an hour.
9:48am - There's also concern about potentially harmful material stored at an old paper mill on the banks of the Mataura.
Gore District Mayor Tracy Hicks says crews are trying to protect the mill from water.
"There have been measures taken to make sure it's as secure as possible," he told Newshub.
9:45am - The message from Emergency Management Southland is to not drive or walk through any flood waters.
"The water may have washed away parts of the road and may contain debris," a post on its Facebook page says.
"Treat all flood water as contaminated and unsafe."
Civil Defence says the evacuation of Gore and Mataura is ongoing.
9:40am - Gore District Mayor Tracy Hicks says a lot of preparations have been put in place.
"The flood event has been predicted to come forward," he says.
"We were looking at midday today [Wednesday], we're now looking at just after 8 o'clock [am].
9:38am - Evacuations are continuing in the Gore district as river levels peak.
People are being urged to conserve water.
9:35am - The main bridge linking east and west Gore has been closed with water pushing against it due to the flooding.
Gore District Mayor Tracy Hicks says the bridge isn't designed for that.
"As long as the weather doesn't get any higher or stronger, hopefully everything will be okay," he told Newshub.
9:05am - Residents of Wyndham and surrounding low-lying areas are now being told to evacuate immediately.
Civil Defence says residents should go to the Mokoreta Hall with key personal belongings.
8:43am - WeatherWatch warns showers will spread into Otago from Wednesday morning.
A heavy rain warning is in place for the central Otago region and Dunedin.
8:38am - The rest of New Zealand, meanwhile, can expect less than summery conditions on Wednesday.
"Cooler air over the country today [Wednesday] will keep temperatures a little more modest," MetService said on Twitter.
Read more here.
8:35am - In Clutha meanwhile, Mayor Bryan Cadogan is pleading with people to use their commonsense when it comes to flooded roads in the area.
"We certainly had people that were just driving straight through the 'closed' signs," he told Newshub.
"Drive to the conditions, follow the instructions - there are just so many roads closed over the district."
8:30am - Flood river levels are peaking in Gore. Civil Defence Controller Angus McKay says the Mataura River is spilling over.
"We need people in Gore and Mataura to move out of that low-lying area now, immediately," he told The AM Show.
8:29am - Fiordland can expect a few showers on Wednesday afternoon which will move on to Southland by evening, according to WeatherWatch.
8:24am - Civil Defence says power has been cut to the east Gore flooding area and will soon be cut to all evacuation zones in the area.
"Please continue to follow all evacuation instructions," Emergency Management Southland said on Facebook.
8:03am - The next 48 hours will bring much drier conditions to the Southland region, WeatherWatch says.
7:59am - MetService currently has two weather warnings in place for the lower South Island, with heavy rain expected in central Otago and Dunedin.
7:52am - Civil Defence Controller Angus McKay says Wyndham residents also need to be on alert as Mataura River keeps spilling over.
"In the next couple of hours we'll know what the situation is," he told The AM Show.
"People in Wyndham need to get ready."
7:47am - Buses will be departing from Mataura's Presbyterian Church about 8:30am and from the Mataura Community Centre between 8:30am and 9am, Civil Defence says.
"These will evacuate residents and do round trips," Emergency Management Southland said in a statement.
"If you are evacuating pets, ensure they are contained on a leash or in a cage and that you have food for them.
"Stay away from flooded areas until Civil Defence gives the all clear."
7:43am - Emergency Management Southland says the main bridge in Gore will be closed shortly.
People are urged check on neighbours before evacuationg.
"Call 111 if you are in danger," Civil Defence said in a statement.
7:30am - Civil Defence Controller Angus McKay told The AM Show it's the biggest flood for the area in our lifetime.
"It's kind of that one in 100 year event," he says. "We haven't had a flood like this for a long time but this is a serious issue and people need to evacuate."
7:21am - Civil Defence Controller Angus McKay says the matter is urgent.
"If you need help for evacuation then talk to one of the wardens that's on the street," McKay told The Am Show. "If you can't see a warden, ring 111."
7:16am - Gore District Mayor Tracy Hicks told The AM Show there is concern about the Mataura River.
"We're expecting a reasonably major flood event. It's looking at similar sort of levels to what we had about 40 years ago - there will be quite a lot of people who recall that and know that's a serious situation."
6:21am - "People should go and stay with friends and family on higher ground," Emergency Management Southland said in a statement.
Parts of roads in the area have been washed away and people are being urged to stay away from any flooded areas.
Schools in Gore have been closed for the day and Emergency Management Southland controller Angus McKay said people should avoid unnecessary travel.
On Tuesday, Civil Defence declared a state of emergency in the Southland region. That followed the declaration of a state of emergency in Fiordland on Monday.
Farmers are being urged to move livestock and sandbags were put down overnight.
A welfare centre has been set up at Calvin Community Church.
"If you don't have a place to go, please evacuate to either the Calvin Community Hub on Robertson St or the Croydon Lodge," Civil Defence says.