The Aurora Energy website said at 4.15pm that power was out to about 1200 customers, mainly in Wānaka, the Queensberry/Luggate area and St Bathans.
Parts of Alexandra, Cromwell and Roxburgh South were earlier also without power due to the strong winds.
"Aurora Energy's crews are patrolling the lines and will make repairs to restore power as soon as it's safe to do so," a Queenstown Lakes District Council statement said.
No evacuations have yet taken place, the Gore District Council (GDC) said.
Mayor Ben Bell urged residents to stay indoors and avoid travel while council staff worked overtime filling sandbags and pumping water.
Consistent rain is expected to continue in the area until at least 5pm.
The GDC has put out a call for help filling sandbags as they are overwhelmed with requests from people in Gore and Mataura.
About 4.30pm the Clutha District Council advised of road surface flooding in the Catlins and Clinton/Waipahi areas.
A CDC spokeswoman said many stormwater structures were at or close to capacity, which has resulted in water backing up on roads.
Contractors have had reports of flooding across Hunt Rd (Catlins), Slopedown Rd, School Rd/Railway Tce Waipahi, Papatowai Highway.
The Papatowai Highway was in the process of being closed at the bottom of Caberfeidh hill (between Burnt Flat and Mouats Saddle intersections) due to the high river running over the road.
Speaking on the campaign trail in Napier earlier, Prime Minister Chris Hipkins said he was aware of the flooding in the South and that NEMA would be providing further updates.
"I'd just encourage people in that region to follow the guidance, keep an eye on the weather report and follow the guidance of the local national emergency responders," he said.
This morning, a general flood warning was issued by Southland District Council.
"Our contractors are getting to as many call-outs as they can, but the surface flooding is widespread and they are unlikely to be able to respond to every report immediately," SDC spokesman Chris Chilton said.
In Central Otago, it is the wind doing the majority of the damage.
Alexandra Blossom festival event manager Martin McPherson said organisers were watching the weather closely.
"We've got fingers and toes crossed that the weather doesn't let us down," he said.
At least six roads were closed due to fallen trees, including SH6 at Mount Pisa Rd near Luggate, and Central Otago District Council is warning of windblown debris making driving hazardous.
Lowburn Valley Rd, Swann Rd, Antrim St in Cromwell, Kelliher Lane and Burn Cottage Rd were all closed but reopened at about 2.30pm.
Further north near Makarora, Muddy Creek has flooded on to State Highway 6, covering the road in earth and debris.
Frances Adank of Waka Kotahi said the road between Makarora and Haast was closed and it could take hours to clear.
Heavy rain is forecast throughout the South today as a major front makes its way up the country.
A heavy snow watch was added to the raft of heavy rain and strong wind warnings this morning.
Heavy rain in the region is expected to turn to snow above 500m with heavy snowfall possible above 700m.
Heavy rain warnings are in place for the headwaters of Otago lakes and rivers, Fiordland, Southland and Clutha.
Up to 300mm of rain is expected in the Southern Alps with possible thunderstorms accompanying lower levels further east.
Southland and Clutha can expect 50 to 80mm of rain, especially northwest of Lumsden until about 6pm today. Peak rates of 10 to 15 mm/h are likely.
The rest of Otago, including Dunedin, is under a heavy rain watch for 24 hours from 11am today.
The heaviest rain is expected to fall this afternoon as a southerly kicks in and sends temperatures plummeting from 20degC this morning to 10degC by 6pm.
Balclutha (26.2), Oban in Stewart Island(23.5), Orari near Ashburton (28.2) and Tautuku in the Catlins (25.6) all hit their warmest September day on record yesterday.
It was Dunedin's warmest September day in 14 years, reaching 24.7degC.
