The incident came to light after the minor complained of pain and was referred for medical examination.
Several parents and locals protested outside the school on Monday night questioning the negligence on the part of the school management.
As the situation turned tense, chief minister Manohar Parrikar visited the spot late Monday night assuring stern action against the accused.
"We will not spare the accused and anyone involved in this crime," Parrikar said, following which police detained the headmistress.
Police said the culprit is yet to be arrested. A sketch has been prepared based on the description provided by the victim, they said.
Incidentally, the school has been one of the well guarded institute with Central Industrial Security Force (CISF) personnel posted at the gate.