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Deputy rector Mark Hooper said the group of about 25 year-nine pupils were scheduled to return today but the creek rose rapidly and became too high to cross.
All parents had been informed and there was ample food in the hut in the Matukituki Valley, he said.
It was hoped the party would be able to walk out tomorrow to a waiting bus.
A heavy rain warning was in place for headwaters of Otago lakes and rivers, which includes the Matukituki Valley, until 1pm today.
Heavy weather is battering much of New Zealand, closing a West Coast highway and prompting Civil Defence to activate in Westland.
MetService said Hokitika copped more than 800 lightning strikes in a 20-minute period this morning.
The weather also prompted a warning from the Mountain Safety Council for people planning backcountry trips in Aoraki/Mt Cook and Arthur's Pass.
Heavy rain in the Southern Alps was expected to significantly change the snowpack and has seen both Aoraki/Mt Cook and Arthur's Pass regions upgraded to ‘High/Don’t Go’ danger on the NZ Avalanche Advisory, the council said.
“Heavy rain and severe gale winds make for dangerous conditions to travel in, both from avalanche risk and exposure possibilities.
“Very heavy rain to above 3000m will saturate an already wet snowpack creating a high likelihood of extensive wet loose avalanching on all aspects.
"Backcountry travel is not advised in Aoraki/Mt Cook and Arthur's Pass at this time."