The father said he has decided to shift both his daughters to another school in Vasco town.
The seven-year-old girl was raped inside the school toilet in Vasco town of Goa on January 14 this year.
The accused is still at large, while a special investigation team of the police has failed to crack the case.
The parents of victim girl had earlier approached Goa State Commission for Protection of Child Rights, a state-government run body, after both the girls refused to attend the classes being under trauma.
"It was only after we approached the commission that the education department, through its order dated March 4, 2013, has directed the school to promote both the students without appearing for the exam," he said.