"Investigation is going on. I have told the police to take action against the institution," the Chief Minister said.
A criminal case has been filed against the school and an attendant has been detained and is being questioned.
The police say the school has been booked for running classes beyond the sanctioned limit; it reportedly had a licence to run only classes 1 to 5. But the school is allegedly running the nursery section and Classes 6 and 7 illegally.
The father of the child has alleged that she was attacked in school. Her mother says she found her daughter crying when she went to pick her up. The child had signs of fever and complained to her mother that she was "physically abused by someone she did not know or recognize," the police complaint said.
The Chief Minister said after three incidents of children being attacked in school in four months, his government's concern was at the "top level."
The case led to large street protests in the IT city by parents and activists and inspired a series of safety measures in schools including CCTV cameras.
Nearly 200 schools in Bangalore were booked for not having safety measures in place and were ordered to make massive changes for the protection of students.
A fresh wave of anger swept Bangalore this week after the new case of a child's rape in school was reported.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.