The pupil at Balswin girls' high school in Bangalore city, Karnataka state, was ordered to run three times around the school and twice up and down the stairs, after turning up late for a PE class.
After two rounds, Bhagyashree complained to the PE teacher, but was told to carry on, following which she collapsed and died.
Karnataka's minister for primary and secondary education said the autopsy report suggested that the girl had been punished soon after lunch and could have died on the food she regurgitated due to physical stress.
He said the government is taking the issue very seriously and has issued guidelines warning against physical exertion for pupils soon after the midday break or in the heat. Teachers have also been told to avoid punishing pupils with strenuous exercises.