A state of emergency has been declared in Dunedin, 800 homes are at risk of being inundated with untreated sewage and the council is making plans to evacuate people from South Dunedin.

Residents of a South Dunedin rest home are being evacuated after torrential rain caused flooding and continues to lash the city.

Managing Director of Radius Care Brien Cree said their primary goal was the safety of the staff and patients at Radius Fulton Home.

Patients were being moved with the assistance of local DHB, Civil Defence, emergency services and family members, he said.

"Management at Radius Fulton is being well supported and we have activated our contingency emergency plans and are confident of a safe and speedy evacuation of the premises." said Cree.

Around 800 Dunedin homes are at risk of being inundated with sewage-contaminated floodwater.

Mayor of Dunedin Dave Cull declared a state of emergency at 2.20pm to make sure extra powers were available to assist in the emergency response.

There was now "significant flooding" across Dunedin and the city's infrastructure was being overwhelmed in places, including South Dunedin and Mosgiel.

Dunedin Civil Defence Controller Sandy Graham says Civil Defence was making plans to evacuate people from South Dunedin if required, as heavy rain forces wastewater into streets.

"The volume of rain we have had is overwhelming parts of the network.

"That means in some places stormwater has entered the wastewater system, forcing wastewater on to some streets."

Police are visiting properties affected by wastewater overflows around South Dunedin to let people know that an evacuation centre is available if needed.

A centre has been set up in South Dunedin at the Caledonian Gym building, Andersons Bay Road for anyone who wishes to leave their home.

An information centre is open in Mosgiel at the Memorial Park Hall, Gordon Road.

Water is beginning to enter sections in Surrey St where sandbagging is taking place and also on Macandrew Rd at the Forbury Rd end. Malvern St in Leith Valley is also flooding.

The Otago Regional Council has issued a flood warning for the Water of Leith and Lindsay Creek and says there is a risk they could overflow into residential areas.

Cull said there was now significant flooding in areas across Dunedin, particularly in South Dunedin and Mosgiel.

"We will continue to keep the community informed and we are doing everything we can to keep people and properties safe."

Around 36mm of rain fell in Dunedin in the two hours up to 2.50pm and rain was still falling.

The rain was expected to ease significantly by around 6pm, but it will take some time for floodwaters to recede.

The DCC, Otago Regional Council, emergency services and contractors were working "flat out" to deal with as many issues as possibly as quickly as possible.

"We are asking people to avoid travel in affected areas if possible.

"Anyone who needs to drive through streets with surface flooding should slow down to reduce the amount of floodwater washed into property or businesses."

Parts of Surrey St were completely under water and there was severe flooding on nearby Wycolla Ave.

A call has been put out for people to help fill sandbags at Mosgiel Memorial Gym car park.

Some Mosgiel shops have also experienced flooding.

A mud slide caused by a blocked culvert has brought rocks and debris down on to Lindsay Rd in Caversham, blocking it.

There was also fallen branches and trees, and rocks on the roads.

Senior Sergeant Brian Benn said a large number of roads across the district which are closed or affected.

SH8 was closed between the Millers Flat Bridge and Scotland Street in Roxburgh due to flooding at Black Jacks Creek, Snr Sgt Benn said.

There are a number of slips and rock fall on SH8 between Clyde and Cromwell and SH6 between Cromwell and Queenstown.

There was also "severe surface flooding" across South Dunedin and a number of roads were closed.

Portsmouth Dr and Portobello Rd were down to a single lane and high tide is expected around 5pm.

"This means the flooding will still increase so we ask that people avoid these waterfront areas and riverbanks, particularly the Leith River in north Dunedin.

"Traffic is also building up in central Mosgiel as Gordon Road is currently closed between Cargill Street and Factory Road due to surface flooding.

"There are limited diversions so we ask that motorists stay away from this part of town," he said.

Earlier Civil Defence said Otago Peninsula and West Harbour residents should consider heading home early ''for safety reasons''.

The warning for residents to go home early comes after several schools closed early for the day owing to flooding concerns as the city is battered by ex-Cyclone Fehi.

Dunedin experienced the country's highest temperature of close to 35C yesterday but today is being hammered by rains as the storm sweeps the country.

Schools that have closed early include: King's High School, Queen's High School, Bathgate Park, St Clair School and Tahuna Normal Intermediate.

In Central Otago, some pupils had been sent home early from Roxburgh Area School on school buses.

By midday, 46.4mm of rain had fallen in the city. A king tide is due about 5pm, which would raise the groundwater level in places, Civil Defence said.

Fire and Emergency New Zealand spokesman Joss Debreceny said emergency services were preparing sand bags for Radius Fulton Home after water began entering the Caversham premises.

They had advised management to evacuate residents from the building, he said.

Several roads are closed around the city and the DCC is advising motorists to take care.

Sandbags were available in South Dunedin from the carpark behind the St Clair Tennis Club and in Mosgiel from the Memorial Park carpark.

Queenstown Lakes District was reporting significant flooding on Mt Aspiring Road outside Wanaka between Mt Roy carpark and the lake front near Ruby Island, and the road may be closed this afternoon.

Several roads at the head of Lake Wakatipu are also closed.

Central Otago District Council was warning of fallen trees in the Maniototo, as well as surface flooding on roads across the district.

The latest MetService heavy raining warning for Otago issued at 10.14am predicted 80mm to 150mm (up from the 130mm predicted yesterday) of rain to fall between 2am and midnight tonight.

More rain was possible in western parts of Otago.

A strong wind watch is also in place for North Otago, Dunedin and Clutha until midnight tonight.

MetService has also issued road snowfall warnings for the Crown Range Rd and State Highway 8 (Lindis Pass).

Severe weather is also expected in Southland and other parts of New Zealand. Peak intensities of 15mm to 30mm per hour were forecast.

Emergency Management Otago director Chris Hawker said firefighters left "very tired" after spending hours battling yesterday's massive blaze in Burnside are now on call and ready to respond to flood related damage in the city.

He had spoken Fire and Emergency New Zealand, which was "very aware" of flooding issues and had firefighters available to respond.

After a "very intense" 24 hours fighting the Burnside blaze and other fires exacerbated by yesterday's heat and wind, they faced the likelihood of another busy day, but Mr Hawker was confident they would be up to it.

"They have got a lot of very tired people."

Wastewater discharges

As a result of the heavy rain, there are some minor wastewater overflows to waterways around the city. These are emergency overflows to prevent wastewater backing up and running on to private property or roads.

As a precaution, the emergency outfall at Lawyers Head has been opened to alleviate pressure on the Tahuna wastewater treatment plant.

A power outage in West Harbour means two wastewater pump stations are discharging into the Otago Harbour. This discharge will stop when the power is restored.

West Coast roads warning

Several roads are closed and strong wind warnings are in place across many parts of the South Island today.

The New Zealand Transport Agency strongly advised users crossing the alpine passes, especially SH73 and the Coastal SH6, to avoid travel unless essential due to the deteriorating weather.

Parts of SH6 have closed this afternoon due to strong winds: SH 6 Westport to Greymouth (Westport to Rapahoe), SH 6 Inanagahua Jnc to Westport and SH6 Hokitika to Makarora.

The South Island storm is a significant weather event and the combination of rain, wind and storm surge is causing streams and rivers to rise, flooding, slips and coastal inundation, and trees to topple, making driving hazardous.

Southland

The New Zealand Transport Agency says road users should take care on State Highway 94 (Te Anau Downs to Fiordland National Park) due to heavy rain and drive to the conditions.

Queenstown

The Queenstown Lakes District Council advised this morning that the Mt Aspiring Rd is closed past the Treble Cone turnoff due to surface flooding.

Paradise Rd is closed at the Priory Road intersection as the first ford at Jordan Creek is impassable. It will remain closed until river flows have dropped and the roading team can repair it.

Clutha District

There have been no reports of flooding or other issues following heavy rain overnight, the Clutha District Council said late this morning.

However, local Civil Defence staff would continue to monitor the situation and work with Otago Emergency Management staff as needed.

The council said people should take usual precautions, including keeping an eye on streams and rivers that could rise rapidly, and driving to the conditions.

Current water restrictions remain in place, it said, as the intensity of the rain and runoff may affect treatment plants ability to produce water. The council would keep a close eye on water schemes in the next day or so.