More than 700mm of rain has fallen in the region over the past three days, causing the worst flooding in 10 years. Extensive tracts of low-lying farmland are flooded with many roads closed.
The flooding knocked out phone lines to Te Anau, prompted the evacuation of trampers and caused the closure of roads and schools.
The Mataura River was predicted to reach its peak at Gore about 1.30pm but it was not expected to threaten stopbanks there or at Mataura, Wyndham or Edendale.
However, farmers in the Lower Mataura area have been advised by Environment Southland to move their stock.
Flood peaks were in the lower reaches of the region's other major rivers, said council incident controller Warren Tuckey.
It would take several days for catchment staff to be able to assess all the stopbanks but there had been only one report so far of a bank being breached by floodwaters - on the Oreti River near Dipton, he said.
Council staff were starting to compile reports of damage from other areas, including the Te Anau Basin as floodwaters slowly receded.
Many roads in the region remained closed by surface flooding and drivers were urged to get up-to-date information before travelling.
MetService is forecasting another front to hit the West Coast of the South Island over the next couple of days, dropping more rain on already saturated land.
High levels on the Oreti River near Winton, where it was feared the river would breach floodbanks, passed without incident early today, Civil Defence Controller Neil Cruickshank said.
The peak of the Oreti River reached Wallacetown at 5am, 4.01m above normal.
Wallacetown farmer Dave Marshall told Radio New Zealand this morning the council had misinformed farmers and the river was still rising.
Stopbanks had been breached and "two or three" dairy farmers had been caught out, Mr Marshall said.
"They've misinformed people. They were on the radio an hour ago saying there wasn't going to be any problems and there's a few major problems around Wallacetown."
State Highway 94 at Whitestone near Te Anau remains closed and there is a possibility that State Highway 6 to Queenstown and State Highway 99 to Riverton at Makarewa River will flood, he said.
It is unclear at this stage is these roads will be able to remain open.
Meanwhile, residential phonelines knocked out by major flooding in Te Anau and Fiordland in the deep south have been partially restored.
Landline services in and out of Te Anau were restored to most households via an alternative radio link about 7.30pm last night, Chorus spokesman Brett Jackson said.
The area has been inundated with rain for over three days, forcing road closures and the evacuation of more than 100 trampers.
Mr Jackson said the main fibre optic cable, which was cut about 1.30pm yesterday due to flooding at Whitestone River Bridge on State Highway 94, would be assessed this morning.
About 100 households near the bridge were still without phone services, he said.
"Technicians are now focusing on the gradual restoration of mobile voice services to mobile sites in the Te Anau area by utilising the radio link," he said.
Broadband services to Te Anau were unlikely to be restored until the main fibre route was repaired.
The MetService has lifted heavy rain warnings for inland Southland north of Winton and Mataura.
Heavy rain would continue in Westland and Fiordland until early Wednesday morning, with significant spillover into the headwaters of the Canterbury and Otago lakes and rivers.
Rivers and steams in Westland and Fiordland were expected to rise further, along with rivers in Canterbury and Otago which fed from the Southern Alps.
Up to 25mm of rain was expected in inland Southland and central Otago this morning.
Meanwhile, the first of about 120 trampers were yesterday evacuated from parts of Fiordland flooded by the weekend rain.
Department of Conservation programme manager Ross Kerr said 120 trampers on the Milford Track had been holed up in three huts for two nights, but diminishing food supplies meant evacuations were necessary.
The trampers were being flown out of the area and delivered to the head of Lake Te Anau, where boats would ferry them to town.
Flooding has caused extensive damage to fences and other infrastructure on farms in the Te Anau Basin, while river levels continued to rise across Southland, Environment Southland said.
Environment Southland's hydrologists were monitoring the rivers and modelling the impact that further predicted heavy rain would have on already high water levels.
The flooding prompted the Southland civil defence emergency management group to advise motorists against nonessential travel.
