The guidelines were being framed and would be circulated to all the schools, a senior education department official said.
The crux of the guidelines would be that the school should be responsible for the safety of the students, he said.
"The student is in the custody of the school management, not parents, during school hours. So it is their responsibility to ensure that they are safe," the official said, on condition of anonymity.
A seven-year-old girl was raped inside the school toilet in Vasco town on Monday morning, sparking outrage among the parents and locals.
The accused is yet to be traced by police, even as the headmistress of the school was taken in custody for negligence.
The department is also preparing a detailed report about the incident, which would be submitted to the state government, the official said.