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 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.
Reddi said Kerawalla was arrested in Daman and brought here this morning. He would be produced before court within 24 hours and they would seek police custody to pursue the investigation further.
Countering charges that there was a delay in arrests, he said, "Arrests are always done on time and pronto. We always do things pronto. That is an assumptive question and you are asking me there is a delay - there is no delay. I am saying there is no delay."
Asked whether other staff members were also involved in the crime, Reddi said, "Gentleman, we will not leave any stone unturned."
Expressing disappointment over some media reports suggesting that there was a cover up in the high-profile case, he said, "There are some reports in the papers using the word 'cover-up' - that has hurt us."
Meanwhile, Akhil Bharatiya Vidhyarthi Parishad activists protested against Chief Minister Siddaramaiah's comments to the media on the case.
Siddaramaiah had yesterday courted a fresh controversy in the Vibgyor case when he asked the media if it did not have any other issue to cover.
"Except that, don't you have any other issue Is this the only news you have Siddaramaiah had snapped back at reporters who sought to know the latest on the case that has evoked public outrage and drawn criticism of his government for not
ABVP activists also tried to lay siege to Siddaramaiah's residence, but their attempt was foiled by police, who detained them.