Officials are beginning to count the cost of cleaning up after this week's dramatic flooding across the lower South Island as evacuated residents return home to face the damage.

Affected councils in Gore, Clutha, Southland and Queenstown-Lakes have done early assessments of damage to key infrastructure, which range from "significant" in Southland to "not the most severe" in Clutha.

Total costs are expected to run into millions of dollars, although most authorities have been reluctant to place a figure on repairs while a state of emergency remains in place across the region.

The Mataura River's water laps about road-working machinery on Wednesday. Photo / Stephen Jaquiery
The Mataura River's water laps about road-working machinery on Wednesday. Photo / Stephen Jaquiery

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Floodwater inundated large parts of Fiordland, Northern, Central and Eastern Southland and South and West Otago between Monday and Wednesday, leading to multiple highway and road closures and causing Gore to be cut off for more than 24 hours.

People evacuated from Mataura were able to start returning to their homes yesterday afternoon. Most people evacuated from Gore — except from a still-flooded Ontario St — returned late on Wednesday.

Mataura people returned to find surface flooding still evident in Main, Oakland, Bangor, Bristol, Carteret, Dover, Carlyle and McConnell Sts. Power to some properties had been disconnected.

The Mataura River flows across farmland near Gore. Photo / Stephen Jaquiery
The Mataura River flows across farmland near Gore. Photo / Stephen Jaquiery

An unknown number of properties were likely inundated or uninhabitable.

Gore District Council deputy chief executive Ian Davidson-Watts said council staff were working hard to get people back into the properties. Pumps were clearing Ontario St, which remained isolated.

Gore Mayor Tracy Hicks was pleased Mataura people could begin to return after many expressed frustration with the evacuation.

The Mataura River rises to cover parts of Gore on Wednesday. Photo / Stephen Jaquiery
The Mataura River rises to cover parts of Gore on Wednesday. Photo / Stephen Jaquiery

"Any dislocation to homes causes frustration. People desire information and they want to know if they can get back to it [their home]," he said.

About 1500 people in Mataura were forced to abandon their properties on Wednesday as a churning Mataura River broke its banks.

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Hicks confirmed the gravity of the event: "My understanding is that [on Wednesday] in Gore and Mataura, there was more water that went down the channel than there has ever been before."

The Mataura River peaked at 2500cumecs at Gore River, and at nearly 2700cumecs at Mataura.

A utility vehicle sits in front of a flooded house, where it was left as the water rose. Photo / Stephen Jaquiery
A utility vehicle sits in front of a flooded house, where it was left as the water rose. Photo / Stephen Jaquiery

A boil-water notice was issued for Mataura as a "precautionary measure", Hicks said.

A water tanker would provide fresh water and a welfare centre would be set up to provide information and resources.

The cost of repairing infrastructure was not known yet.

"In essence, we've had two events in one here, with huge run-off from local rain combined with issues with extreme river flow," Hicks said.

"Roads, culverts and pumping stations have all required attention, but our focus at the moment remains getting people safely back in their homes."

The swollen Mataura River rips through the town on Wednesday. Photo / Stephen Jaquiery
The swollen Mataura River rips through the town on Wednesday. Photo / Stephen Jaquiery

Southland Mayor Gary Tong said he believed final costs would run into "millions".

"The guts of it is this is a significant event, which will require a significant amount of work to make things safe again. Compared to damage from past flood events, it's right up there."

Although roads had been severely damaged across the region, "3 waters" infrastructure remained unaffected: "Luckily we've dodged that bullet."

Clutha district incident controller John Scott said it would take "some time" to assess the district's 3000km of roads.

"Although early feedback suggests we've not experienced the most severe damage historically, there's a lot of work to do. We're just trying to get traffic moving as safely as possible."

The roofs of parked cars peek above the floodwater in Gore on Wednesday. Photo / Stephen Jaquiery
The roofs of parked cars peek above the floodwater in Gore on Wednesday. Photo / Stephen Jaquiery

He did not believe the eventual costs would be "huge" for the district.

A Queenstown Lakes District Council spokeswoman said staff were not assessing road or infrastructure damage during yesterday's statutory holiday, but would resume inspections this morning.

A council statement on its website on Wednesday said a clean-up was under way to address "minor slips and surface flooding".

Seven roads remained closed across Queenstown-Lakes at 5pm yesterday.

In Southland, 35 roads remained closed, in Clutha the number was 30 and in the Gore district 15 were yet to reopen.

State Highway 94 towards Milford Sound was damaged in many places during the week.
State Highway 94 towards Milford Sound was damaged in many places during the week.

Some state highways remained closed yesterday afternoon, although most had reopened.

State Highway 1 through Mataura to Gore reopened with a 30kmh speed restriction. State Highway 93 from Clinton to Mataura was also reopened.

State Highway 99 from Lorneville to Wallacetown remained closed.

The NZ Transport Agency said the full length of the Milford Rd was unlikely to be open before Wednesday next week, and possibly would be closed longer, due to extensive damage beyond the Main Divide.

Multiple serious slips and road washouts are apparent from photographs posted by the NZTA this week, but NZTA system manager Graeme Hall said the agency needed more time to work out exactly what would be required to fix the road.

"At the moment, we are in response and assessment stages so it will be several days before we properly understand the costs and programme of works."

The NZTA reopened SH94 from Te Anau to Cascade Creek yesterday, and expected to extend that as far as the Hollyford turnoff or the Main Divide by this afternoon.