The headmistress was arrested yesterday for negligence.
Judicial Magistrate First Class (JMFC) Vasco remanded Mormugao Port Trust-run school's headmistress Sharlet Furtado in seven-day police remand.
Police have booked Furtado for negligence on her part which resulted in the rape of the seven-year-old girl in the school toilet.
Crime branch, which is investigating the case, has also booked a case against school authorities for destruction of evidence after the management allegedly gave bath to the girl, washed her clothes and cleaned the toilet after the rape.
The January 14 rape offence sparked outrage with people protesting on the streets demanding justice.
Goa police formed a 15-member special investigation team to probe the case.
The sketch of the accused, suspected to be a middle-aged man, has been released by police to trace him.