The Milford Track is closed by bad weather for the second time in two weeks after the Clinton River burst its banks.
The Department of Conservation said the more than 100 trampers currently on the Milford Track are safe in huts and will remain there until the weather subsides.
DoC spokesperson Annie Wallace said they include several families with children.
An assessment of all tracks in Fiordland will be made on Thursday morning.
Heavy rain in Fiordland forced DoC to close the track on New Year's Day forcing 120 trampers to stay an extra night.
More than 400mm of rain fell on the western side of the 53.5km route on New Year's Eve.
In March 2010, 120 trampers were airlifted from the track after a storm. Twenty people were also taken off the Routeburn Track.