The girl was allegedly sexually abused in the school toilet by the accused on Tuesday.
The victim complained of pain to her mother on Tuesday evening after she returned from the school, police inspector CL Patil told reporters.
"The girl was referred for medical examination which confirmed sexual abuse," he said.
The incident comes days after a seven-year-old girl was raped in a school toilet in Vasco town.
The parents of the victim in Vasco town had said that the girl was given a bath, her inner clothes were washed and toilet was cleaned after the rape, destroying the evidence.