The Department of Public Instruction in a release said the state government had written to the ICSE to derecognise Vibgyor High School and that the DPI Deputy Director (South Division) is inquiring into the incident.
"The inquiry is on," it said.
The rape had triggered severe protests from outraged parents who stormed the institution yesterday, demanding action against the guilty, suspecting the involvement of staffers.
The girl was allegedly raped by "unknown persons" at Vibgyor High School, which came to light on July 15.
The issue also figured in the assembly where former Education Minister Vishweshwar Hegde Kageri (BJP) sought a reply from the government on police allegedly caning the agitating parents who were protesting the "inaction" by school management.