Villagers protested outside the school gate and did not allow it to be opened, police said.
Officials, who reached the spot to pacify the villagers, said that apart from the accused, the school principal has also been arrested and the entire staff has been transferred.
The 15-year-old girl was allegedly raped by Rajinder Singh several times during the last one month at gunpoint.
On May 16, the accused was arrested following a complaint lodged by the victim's parents.