Warnings and watches for heavy rain across much of Otago and Southland, but the area expected to be most affected is Westland and Fiordland south of Hokitka where the MetService has upgraded the warning level to a "red warning" from orange.
Areas of low lying Fiordland have started evacuations and the Milford Rd was expected to remain closed for some days.
The Milford Road Alliance says flooding is causing "significant damage" with rainfall rates of 55mm an hour.
The alliance was checking the road for vehicles.
The MetService said the event had high potential for "further significant impacts, such as major slips, road closures and flooding, in the next 24 to 36 hours.
"This decision was made in consultation between Metservice Meteorologists and West Coast Regional Council Hydrologists and Civil Defence Officers."
A series of fronts were forecast to move east across the South Island from yesterday morning through into tomorrow afternoon, bringing periods of heavy rain to the west and the south of the South Island and strong west-to-northwest winds to parts of southern and central New Zealand.
A MetService spokesman said a a heavy rain warning is in force for Fiordland, Westland, the headwaters of Otago Lakes and Rivers, Southland and Clutha.
The heavy rain watch for Central Otago, the Southern Lakes and the headwaters of the Canterbury lakes and rivers have now been upgraded to an orange warning. Watches for heavy rain have now been issued for Dunedin and Buller.
"Heavy rain may cause streams and rivers to rise rapidly. Surface flooding and slips are also possible and driving conditions may be hazardous."
In the headwaters of the Otago lakes and rivers, up to 450mm of rain is expected to accumulate near the main divide, and up to 280mm is expected within 15km east of the divide until 1pm tomorrow.
Evacuations begin in Fiordland
Low lying areas in Fiordland have been evacuated this morning due to flooding.
A police spokeswoman said police were notified of the flooding in Gravel Pit Lane in Fiordland National Park at 9.10am this morning.
Those who had been evacuated were being directed to the assembly point at Mitre Peak Lodge.
In Fiordland, up to 500mm of rain may accumulate north of Doubtful Sound and up to 300mm further south until 10am tomorrow.
An official Civil Defence Emergency Management Southland (CDEMS) statement confirmed 382 people had been moved to the lodge.
CDEMS controller Angus McKay said the Cleddau River and high tides had caused flooding through the workers' village.
The visitor car parks and terminal car parks were flooded and water had spread across the apron at Deepwater Basin.
Milford Rd was expected to be closed for some days.
Everyone was accounted for and the Milford Track was cleared during the weekend.
The Invercargill emergency centre would be monitoring the area and responding where it was needed.
Mr McKay said response teams were well equipped to deal with the elements.
''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.''
West Coast
The highway between Fox Glacier township and Haast in South Westland reopened this morning after rain washed out a culvert at Thirsty Culvert late yesterday.
An NZ Transport Agency spokesperson said SH6 was closed shortly after 5pm yesterday but re-opened at 9.30am this morning.
The Milford Road SH94 remained closed between Cascade Creek and West Gate (the Chasm).
The NZTA spokesperson said due to flooding in the south of the South Island, SH94 Milford Rd was expected to remain closed all day Monday and Tuesday morning as heavy rain was forecast to keep falling.
In Westland (from Harihari southwards), up to 500mm of rain may accumulate about the ranges, and up to 160mm near the coast until 2pm tomorrow.
Peak rates throughout these regions were generally expected to be up to 25mm an hour and up to 35mm to 40mm if there were thunderstorms, he said.
There is also a strong wind watch in place for eastern parts of southern and central New Zealand.
