The closure comes as rain batters East Otago and Southland this morning, with MetService issuing weather warnings for both regions.
In a post on its Facebook page East Taieri School said the rapidly rising Owhiro Stream posed too much of a risk for the school to open.
"The creek has risen incredibly quickly within the past hour, " it said after 8am.
"We worry that it will continue to rise and would mean that we would have to evacuate the school."
The school's caretaker arrived at the grounds about 6am and saw the stream rise about 15cm during the next hour, principal Jennifer Horgan said.
"The car park was flooded and the creek was over the banks and was still rapidly rising," she said.
It was decided to close the school for the day for safety reasons.
It was expected to reopen tomorrow.
It posted pictures of the creek, which was already beginning to burst its banks and flood the school's grounds
