"We have arrested the accused, Jaishankar, on a complaint by the victim's parents that he had allegedly raped their young daughter twice in the school in Indirangar area," Additional Commissioner of Police Alok Kumar told reporters.
"The school is not following all guidelines that we issued, not enough CCTV camera," Kumar said.
A criminal case was registered against Jaishankar under sections 4 and 6 of the Protection of Children from Sexual Offences Act, 2012 and section 376 of the Indian Penal Code on the complaint, which is based on the victim's version.
"The sexual assault seems to have taken place on two occasions - Oct 28-29. We are questioning the accused for details," Kumar said.
The latest incident comes within days after a three-year-old child was allegedly raped on Oct 21 by an office assistant of a top school.
The accused Gundappa was arrested on Oct 25 and sent to 14 days judicial custody for further investigation.