Authorities are disappointed motorists are ignoring road closure signs as heavy rain continues to make many roads impassable, including part of SH1.
State Highway 94 is closed, isolating the township of Milford Sound.
However, heavy rain is easing in Fiordland this morning, and the warning has been lifted.
People are advised to keep up to date with the latest forecasts in case any changes are made.
In the Clutha District about 50 roads have been affected, but the council is disappointed some motorists are ignoring signs.
"It is very disappointing to note that while council roads are being signed road closed we are finding road users insisting on driving straight past the road closed signs and through the flood waters.
"Road users need to be aware that any damage done to their vehicles on closed roads is not covered by insurance and by driving through the flood waters they are causing additional unnecessary damage to already affected properties."
The council warned it was expecting significant amounts of rain in the next 24 hours on top of the rain that had fallen over the last two days.
MetService forecaster Lewis Ferris said one metre of rain had fallen in 60 hours in Milford Sound, and 600mm of that was in the 24 hours to about 7am today.
"Those are numbers some of our most experienced forecasters haven't seen before," Ferris said.
"So 1000mm in an entire event has been seen before, but to get that in two-and-a-half days has been quite a lot."
The NZ Transport Agency said the highway was closed from Cascade Creek to Chasm due to flooding and extensive damage
"It is expected to remain closed all week. Unlikely to be open to The Divide until Wednesday.
"Major damage has occurred between divide and the tunnel at multiple sites."
Queenstown Lakes
State Highway 6 from Frankton (Remarkables Skifield turnoff) to Lumsden.
SH 97 Mossburn to SH6 intersection is also closed as is SH94 from Mossburn to The Key.
QLDC said Crown Range Road has reopened after being closed due to rockfalls this morning.
"However, with significant rainfall forecast throughout the day there is a high chance of further rockfalls around the district."
Glenorchy Road is now closed near Bob's Cove as there are several trees and rocks on the road requiring heavy machinery. Travel is possible from Queenstown to Bob's Cove but not on to Glenorchy.
Paradise Road (Earnslaw Burn washout) - currently closed at Priory Road / Paradise Road turn off.
Kinloch Road – closed on the Glenorchy side of Dart River Bridge and unlikely to be open today.
Routeburn Road (Scott Creek washout) – road closed and not passable.
Central Otago
Central Otago District Council said Dunstan Rd in Alexandra is closed due to flooding. The road is closed between Chicago St and Symes St.
Traffic Management is in place to identify the detour route via Chicago Street, Ngapara Street and Symes Street.
Clutha District
The Clutha District Council said the district had experienced heavy rain over night causing widespread surface flooding and more was forecast today and there
"Council contracts have been busy overnight checking the conditions of the roading network."
There are extensive road closures in the district and an incomplete list of them can be found here.
Gore District
SH1 from Gore to Clinton is closed due to surface flooding.
The Gore District Council posted to its Facebook page saying several of its roads are closed due to flooding which include:
Waikaka Road, River Road, MacGibbon Road, McDonald Road, Ruia Street, Koa Street.
"There is significant flooding around the District and motorists are urged to drive carefully.
"MetService shows 25.6mm of rain has fallen in Gore since midnight, with a further 30mm forecast."
Southland District
Due to heavy rain and flooding, the following roads have been closed:
Ellis Road between Acton and Lowther, Felton Road, McLean Road, Lora Gorge Road and Henderson Road.
We are keeping a close eye on the following areas that might see further road closures:
Otapiri Area, South Hillend Dipton, Athol Area, Garston Area, Dipton Mossburn and Wreysbush Mossburn.
MetService Warnings
Westland south of Hokitika and Fiordland north of George Sound
Periods of heavy rain and a further 250 to 350mm of rain to accumulate about the ranges on top of what has already fallen, and 80 to 130mm near the coast, mostly with thunderstorms.
The heaviest rain in Fiordland is expected to ease overnight Monday and early Tuesday morning.
"This rain is expected to cause dangerous river conditions and significant flooding. Slips and floodwaters are likely to disrupt travel, making some roads impassable and possibly isolating communities."
The headwaters of Otago lakes and rivers, southern lakes and Central Otago
Periods of heavy rain. Expect a further 70 to 90mm to accumulate on top of what has already fallen while isolated thunderstorms are also possible.
Dunedin
Periods of rain, heavy at times. Expect 60 to 90mm of rain to accumulate.
People are advised to keep up to date with the latest forecasts in case any changes are made.
