An evacuation is beginning for 30 stranded trampers, struck by a landslide at Howden Hut, near Fiordland's Lake Howden.
The helicopters lifted off at 7:40am after having to wait for a break in the weather.
Southland District Mayor, Gary Tong, said he's confident they'll be in and out with the trampers.
"We've got a lot of rain, and the temperatures are reasonably high, so that's causing that low cloud right down into the valley floors really."
Some of the trampers have minor injuries after the landslide hit their hut about 1.30 this morning.
Rescue teams will attempt to evacuate 195 tourists from Milford Sound today after flooding caused road slips and cut access to and from the township yesterday.
About 70 ''stragglers'', located on the Te Anau side of the Homer Tunnel (State Highway 94), were evacuated by helicopter although nearly 500, including tourists and about 300 staff, remained trapped in Milford Sound last night.
Tong says most people have been relatively comfortable overnight.
New Zealand Transport Agency journey manager Peter Brown said a small number of tourists were also taken by helicopter from Forks Bridge, about 1.5km from the Homer Tunnel, yesterday afternoon.
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''There is extensive damage from Lake Gunn to the Homer Tunnel which will delay us opening this road quickly and there is still a section we haven't inspected due to bad weather preventing a flyover.''
A state of emergency was declared by Southland Mayor Gary Tong about 2pm yesterday to allow for a co-ordinated response to the flooding, caused by a combination of high tides and heavy rain.
Civil Defence Emergency Management Southland controller Angus McKay said helicopters airlifted Hollyford Track hikers from two walking huts outside Milford last night.
Those trapped inside Milford were moved to higher ground throughout the day.
Although many took up residence at Mitre Peak Lodge, others remained safe on cruise ships in the dock, he said.
Ultimate Hikes New Zealand general manager Noel Saxon, who manages Mitre Peak Lodge, said those who had been relocated to the lodge were comfortable and dry.
''We don't have 400-odd beds but, if it came to it, we would make do and have enough room to accommodate everyone.''
Despite the threat of increased flooding in the coming days, response teams and businesses in the area were ''well equipped'' to deal with the conditions, he said.
''Milford's really used to this kind of thing. They have the road closed through winter quite a lot so they've got really good practices in place.
''They'll look after everybody and feed everybody and make sure they're warm.''
Tourism operators would be putting plans in place and ''as they can'', would fly out any tourists who urgently needed to get out of Fiordland.
A MetService spokesman said the warning had been upgraded from orange to a red about noon, and more rain was expected over the next day and a-half.
''We expect a further 300mm-350mm of rain to accumulate about the ranges. Those are the upper limits of what we expect will fall. Smaller amounts are expected around the coast, about 90mm-150mm through until 4pm tomorrow.''
A red warning meant the effects would be ''significant'' and further road closures and slips were very likely.
A New Zealand Transport Agency report said significant damage had been caused to the road and rainfall rates were 55mm an hour.
Milford Rd, between Cascade Creek and West Gate (State Highway 94), had also been closed after ''numerous'' slips from consistent rainfall.
An Air Milford spokeswoman said no flights would be sent out until weather conditions were deemed safe, which could be Wednesday ''at the earliest''.
In Dunedin, city council staff and contractors were preparing ahead of the rain, checking and clearing stormwater and wastewater infrastructure.
Residents were advised to check drains, gutters and grates were clear to handle a large downpour.
The Otago Regional Council's duty flood officer, Lauren Hunter, said Lakes Wanaka and Wakatipu were rising, but neither lake was expected to reach flood levels.
River flows were also rising as a result of the heavy and consistent rainfall.
''We are paying close attention to the Dart and Pomahaka Rivers in particular, which are above high flow thresholds.''