"We're just thankful the kids were in classes," principal Linda Miller said of the "out-of-the-blue" whirlwind, which struck the school's quad at 10.20am.
The gust ripped three sheets of corrugated iron roofing off one of the prefabricated classrooms.
"One went clear over trees on the far side of the sports ground - another sheet sliced into the ground in an area where kids are sitting at lunchtime. I think it could have lifted up some of our smaller kids," Ms Miller said.
The school has 220 pupils, from years 7 to 13, and the flash flurry happened so fast "the kids didn't have time to get their cellphones out and take pictures", Ms Miller said.
One of the sheets lodged in the turf, leaving corrugated divots, illustrating the impact and potential danger of the freak weather event, Sergeant Tod Hollebon, of Te Anau, said.
"There was certainly some potential for serious harm - it was a frightening incident. It's just exceedingly fortunate nobody was out and about," he said.
Fiordland had been experiencing "unusual, unseasonal weather patterns" over recent weeks, Sgt Hollebon said.
National Institute of Water and Atmospheric Research (Niwa) principal climate scientist James Renwick said it was "quite windy at the time" and it was "quite possible" a local whirlwind could have come out of "general turbulence".
"It's in a mountainous region with colder, denser air mixing with warmer air, which can start to rotate," he said.
On Wednesday, Manapouri Airport recorded winds gusts of over 70kmh, which could have created a "whirlwind effect", Mr Renwick said.
