The teenage girl, allegedly raped repeatedly by a 60-year-old fruit seller for the past five months, and her two sisters were enrolled in the Government Middle School in a village in Haryana's Fatehbad district.
They were never expelled and left on their own, the school authorities claimed.
Wishing anonymity, a school functionary said "the family of the girls decided to withdraw them from the school and they were not expelled."
The man, who allegedly lured the victim, a student of class six, by offering fruits free of cost, was arrested by police yesterday.
A complaint lodged by mother of the girl with police alleged the man raped her daughter during school hours.
Haryana has witnessed a spurt in cases of rapes during the past two months.