The parents of the two children have demanded CBI probe into the incident, and called for arrest of the class teacher Ambika Nagar.
On Friday, students of the school staged a noisy demonstration demanding action against the teacher and the school management for allegedly torturing the two girls.
The parents said the girls did not die accidentally, but committed suicide after being "tortured" by their teacher.
The girls who died were studying in class 6 and were found dead near the school on Monday. At that time, police said the girls died when a speeding vehicle hit them.
Parents and relatives of the victims on Friday reached the school and staged a protest. They said the girls committed suicide after their class teacher allegedly tortured and mentally harassed them.
"That's the only reason they took the extreme step," one of the relatives told reporters.
Agitated relatives ransacked the school and manhandled staff. Some teachers locked themselves inside classrooms along with students to protect themselves. Pol has been posted incide the school campus.
When the parents and relatives were staging the protest, the school authorities sent SMSs to all the parents to collect their wards immediately as the situation in the school was turning tense.
During the protest, some senior students came out in the support of the victims' parents and raised slogans outside the principal's office.
"The police officials are not fair in their investigation. They are shielding the school management," alleged Rajender Thakur, father of Nancy.
Superintendent of Police Chander Shekhar told IANS that investigations are on. "No case has so far been registered. We are looking into various theories about their death," he said.
The aggrieved parents, however, alleged that they would not be able to get justice unless a case is registered against the class teacher and the school management.
Shyama Jose, principal of the school, said, the school management was fully cooperating with the police. "We are doing our utmost", she said.
Classmates of Sakshi and Nancy told India TV that the girls told them before their death that they were tortured by their teacher Ambika Nagar. One student said, the girls told them the teacher slapped them twice outside their classes, and the two were weeping loudly.