Civil Defence and Southland District Council have a huge task ahead, as they try to contact hundreds of urban and rural residents in the aftermath of the week's flooding.
All of the Southland town was evacuated earlier this week as the Mataura River rose and heavy rain fell.
In the Gore District, at least 21 homes have been damaged by floodwaters and building control officers have assessed the worst affected properties.
Southland Emergency Management controller Marcus Roy said district council officers were visiting rural properties in Edendale and Riversdale before going to the lower Mataura area.
He said they were also looking at how to move into the recovery phase, when the State of Emergency - running until Tuesday - is eventually lifted.
The flooding was arguably unprecedented, he said.
"Effectively, it's been about 30 years since we've had something of this scale and this is probably bigger than anything we've ever had on that catchment to date."
Roy said it was unclear how long Milford would be cut off.
Minister of Conservation Eugenie Sage will fly over the most flood-affected areas of Fiordland today, to assess the damage caused to DOC facilities.
Sage will look at infrastructure, including tracks and huts, and the helicopter will stop at Piopiotahi/Milford Sound where she will meet those involved in the response.
She will also touch down in Te Anau and Queenstown to talk with tourism operators.
A state of emergency was declared in flooded Southland on Tuesday, including Gore, and dozens of people were rescued from tracks in Fiordland after being cut off by torrential rain.
Some of the rescued tourists described a narrow escape with just two minor injuries after a slip swept into the wall of their hut, crushing bunk beds and completely destroying a block of five toilets.
Hundreds more people trapped by flooding and slips in Milford Sound were evacuated by helicopters on Wednesday.
Return of Milford Sound cruise
A Milford Sound cruise company hopes to have boats sailing on the fiord again on Monday.
Cruises have been cancelled all week because of the Southland flooding, which closed Milford Road and cut the remote township off to tourists.
Real Journeys' manager Paul Norris said tourist operators in the area were bound to experience some financial fallout.
"There's no doubt February is one of the busiest months for tourism in New Zealand and in our regions, so it will have a financial implications.
"Conversely, operating in Fiordland, we're always going to be exposed to the weather and that's one of the beauties and reasons people visit out our area."
He said dramatic weather was part of the appeal of Fiordland, but it was disappointing this had happened during one of the busiest months.
Tourists wishing to do a cruise on Milford Sound over the coming week will only be able to get to the area by air.
Potentially toxic chemicals to be moved
A Mataura resident says many locals suspect the risk from toxic waste was the real reason they were made to evacuate this week.
Civil Defence said the risk of flooding was the reason for the evacuation, but it had earlier also acknowledged it was concerned the toxic waste stored at an old paper mill could create ammonia gas if it got wet.
Resident Patrick Kaa said many locals felt in the dark about the real reason the whole town needed to be evacuated.
He said people living up the hill were told to leave, which led many to believe the primary reason was the toxic waste.
Earlier this week, Invercargill mayor Tim Shadbolt said the local councils had been working for years to reduce the risk.
"There has been a movement of some of the dross out of the area but it's a large amount that's being stored at the paper mill and to tackle that is going to require a huge commitment from government as well as local authorities."
Many residents who were evacuated from the town began returning home on Thursday to assess the damage.
A Mataura resident said a large number of locals were calling on the council to remove the toxic waste the day before the flood waters hit.
Gore District Council chief executive Stephen Parry yesterday told the Otago Daily Times that all parties had shaken hands on a deal to transport the chemical elsewhere.
Local resident Gem Burr said the chemical should not have been left in the mill.
She said many locals had commented on the council's social media pages calling for the waste to be moved.
Another resident, Warren Gaudion, said the old paper mill which was being used to store toxic waste was known to flood.
Gaudion said he worked in the old paper mill for years, and over the years saw several floods through the building.
He said when the river rose, it hit a bottle neck and went through the building, and was one of the reasons why the mill was ultimately closed down.