Gales and heavy rain have closed the Milford Track for the second time in just over a week, trapping 89 trampers, including children, in three huts.
The track also closed on New Year's Day, stranding more than 100 trampers for two nights.
The rain in the Clinton Valley had been intense with the river level rising from near normal to above the flood threshold within five hours today, resulting in the Clinton River bursting its bank.
In addition 85mm of rain had fallen in the Arthur Valley in the five hours up to 10am with a further 200mm possible today.
The Mackinnon Pass was also being battered by storm force winds, with wind conditions expected to peak in early this afternoon.
Department of Conservation spokeswoman Annie Wallace said trampers on the Milford Track were safe and well, with most trampers from Dumpling Hut leaving the track today before water levels peaked, and other trampers remaining at the huts for a second night.
"The parties that have decided to remain at Dumpling Hut include families with children.''
Families and operators expecting trampers to return from the track should expect a day's delay until Saturday, Ms Wallace said.
An assessment of track conditions would be made tomorrow morning, and it was expected that trampers could continue as usual from then.
On the Kepler Track, trampers travelling together across the alpine section of the track are being accompanied by the ranger due to high winds and heavy rain, Ms Wallace said.
They were experiencing 60-80kmh winds with the forecast predicting gusts over 100kmh.
MetService meteorologist Daniel Corbett said an active weather system was moving across the South Island.
Fiordland, Westland, some Canterbury and Otago headwaters, as well as parts of Southland could expect up to 400mm of rain by the time it had passed tomorrow, he said.
Strong gales were also passing over the mainland, including a gust at Mt Hutt of about 150kmh, Mr Corbett said.
"We have wind warnings for higher spots in Canterbury.''
Marlborough, Wellington and the Wairarapa could also see gusts of up to 140kmh by tomorrow, he said.
"It'll be one of those dustbin down the road kind of nights in Wellington.''
The northern part of the North Island should not be affected by the extreme weather, he said.