Severe flooding forced thousands of residents in New Zealand's South Island to flee their homes on Wednesday and left hundreds of tourists stranded at the remote Milford Sound beauty spot.

The Southland region declared a state of emergency after being deluged with more than 1,000 mm of rainfall in 60 hours, triggering landslides on major roads and causing rivers to burst their banks.

Authorities told residents in the low-lying areas of Gore and Mataura to evacuate immediately early on Wednesday as floodwaters in the Mataura river peaked, warning those further downstream in Wyndham to prepare to leave.

"We have issued notices to evacuate and to prepare to evacuate to 6,000 people across the region," an Emergency Management Southland (EMS) spokeswoman told AFP.

1104 mm: rainfall since the beginning of February in Milford Sound 🌧️🌧️🌧️



• This is 243% of the February monthly normal & 16% of the annual normal.



• It included Milford Sound's wettest hour on record (60.8 mm). pic.twitter.com/Itldw3daLh — NIWA Weather (@NiwaWeather) February 4, 2020

Residents were advised to grab medication, clothing and identification documents, then head to higher ground.

Floodwaters washed away sections of the only road to Milford Sound, a popular hiking spot for international tourists, and EMS said almost 200 people were being airlifted to nearby Te Anau.

"The tourists... have been well catered for," it said.

Confirming our guests and crew on board the #fiordlandjewel for a third night after a state of emergency was declared yesterday in the #fiordland area are safe, warm and well-fed. At this stage our overnight cruises have been cancelled up to Friday 7 February. #milfordsound #nz pic.twitter.com/xhZgcGNdQw — Fiordland Discovery (@Fiordland_Jewel) February 4, 2020

"Morale has been high amongst the visitors and staff, as they received regular briefings and have been in contact with friends and family."

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Only two minor injuries have been reported after a landslide hit a hut on the Routeburn walking track, with both people receiving treatment at the scene.