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Grave fears are held for the woman, after searchers failed to find her yesterday.
The woman, whose nationality was unconfirmed, had been walking the track with her Australian partner when she was caught in the Pompolona Creek about 3pm on Monday and was swept into the Clinton River, Sub-area Commander Senior Sergeant Cynthia Farley said.
Searches by helicopter yesterday morning and afternoon found no sign of her.
The couple had spent time in Queenstown before ''freedom walking'' the track. The woman's male companion activated an emergency beacon which was picked up by the National Rescue Co-ordination Centre about 6pm.
Maritime New Zealand senior communications and media adviser Steve Rendle said the beacon was activated near the Mintaro Hut, but bad weather prevented a helicopter accessing the area on Monday night. The hut is at the head of the Clinton Valley, about 21.5km from Glade Wharf on Lake Te Anau.
Snr Sgt Farley said a Southern Lakes Helicopter and observer search crew reached the area about 7.30am yesterday, searching the Clinton River and surrounds.
Pompolona Creek was high after recent rain and weather conditions were poor. Rain continued yesterday afternoon and MetService issued a severe weather warning for the area. Between 170mm and 210mm of rain was expected this morning, with ''significant spillover rain'' about the headwaters of Otago lakes and rivers.
''People are advised that driving conditions may be hazardous, rivers and streams may rise rapidly, surface flooding and slips are possible.''
Snr Sgt Farley said police were continuing to search by air, since conditions meant a foot search was ''not feasible''.
Police were working with Department of Conservation staff and LandSAR volunteers. The male tramper was helping with the search effort and was being supported by Victim Support.
The Milford Track Great Walk is closed to guided walkers from May 1 to October 27 but is open to independent trampers with reduced facilities.
''Walkers are advised that alpine skills are essential,'' Snr Sgt Farley said.