Rustom Kerawalla, Chairman of Vibgyor High School, was arrested under various sections of IPC, Juvenile Justice Act and Protection of Children from Sexual Offences Act (POCSO), Bangalore Police Commissioner M N Reddi told reporters here.
Police have invoked section 201 of IPC (causing disappearance of evidence of offence or giving false information to screen offender) against Kerawalla, he said.
This is the second arrest after that of Mustafa, skating instructor as the main accused, on Sunday.
The delay in nabbing the culprits and taking action against the school management had evoked widespread criticism, leading to protests in the city and elsewhere in the last one week.
The incident had happened on July 2 and the complaint was lodged on July 14, while the first arrest came six days later.
As public anger grew, the government had effected a reshuffle at the top police echelon on Monday, transferring Raghavendra Auradkar and bringing in Reddi in his place as Police Commissioner.
The govt changed the city's police commissioner after a public protest
The main accused was sacked at a school earlier for "gross misconduct" with girls, the institution had disclosed, with Vibgyor High School coming in for criticism for not checking the background of its staffer.
Mustafa, who joined Vibgyor High School in 2011, was arrested on Sunday, with police saying they had found pornographic content relating to children in the laptop recovered from him.
Karnataka government has also written to the Council for the Indian School Certificate Examinations Board to derecognise the school.