Weather permitting, almost 200 tourists stranded in Milford Sound are set to be evacuated this afternoon.
The group spent the night at Mitre Peak Lodge or on tourist boats after severe flooding closed Milford Road.
The region received 350mm of rain on Monday, while a further 300-450mm was expected in parts of Fiordland and Westland by Tuesday afternoon.
The group - mainly visitors and staff - were left stranded, with Emergency Management Southland controller Angus McKay saying the plan is to get everyone out on Tuesday.
"As soon as the weather breaks we can get the tourists out from Milford," McKay told Newshub.
"But unfortunately the weather at the moment is not very good, but as soon as we can do that safely we will start that evacuation plan."
The rain had been "pretty steady" through the night, with no sign it will let up on Tuesday, McKay said.
"We've got about 195 tourists and about 300 staff waiting out on Milford Sound - the good news is that the companies in there are well used to the road being blocked every now and then so there's plenty of food and accomodation. Really they're just extending their stay in Milford for another day or so."
He said although the people in Milford Sound were "all safe and well" the concern was for trampers on the Routeburn and Hollyford Tracks.
"The Lake Howden Hut, which is just on the Routeburn Track, there's actually a landslip that affected that building. So we've got about 30 people in there and a couple of them got some minor injuries. They're all still there waiting to be evacuated."
McKay estimated that almost a metre of rain will have fallen by the time conditions improve.
"It's really causing some issues with the landslips, rising rivers - some of the flooding and rain we're having is just out of the box really".
Southland Mayor Gary Tong said for those stranded it was "just a matter of time to get them out". The real concern, he said, was "the welfare of those we don't know [about]."
"We don't know who's on those tracks," he told The AM Show.
"The number one focus is people, so getting the people out of those areas as soon as practically and safely possible. That will start this morning with those that are in the Howden Hut, getting them out. And then checking all the other huts along the track. There's information coming in that there could be people in other parts of Fiordland as well, so we need to check all those."
He added that rain was still "fair dumping down" in the region.
A state of emergency was declared in Fiordland after State Highway 94, between Te Anau and Milford, was cut off due to flooding on Monday.
MetService on Monday issued its first-ever 'red warning' as an onslaught of rain hammered the South Island.
The warning was issued for Westland south of Hokitika and Fiordland north of George Sound.
The warning is reserved for the "most extreme weather events" where "significant impact and disruption" is expected.
McKay says the priority is to get the most vulnerable out first.
"We'll make sure we prioritise people who need to get out or have medical needs, as and when the weather clears. We'll just try to get them out back through to Te Anau as quickly and as safely as we can."
Once rescued, the tourists will be taken back to Te Anau.
"Through the tourist operators, we'll coordinate with them and they'll be using helicopters to bring people out on to the clear side of the road, and then coaches to bring them back to Te Anau."
NZTA said State Highway 94 is expected to remain closed until the end of the week due to the damage caused by the flooding.