"Mustafa, a skating instructor, has been arrested," Bangalore Police Commissioner Raghavendra Auradkar.
Police had been facing mounting public anger over delay in making any arrest in the horrific incident, which had triggered protests in the city.
The protests have taken a political turn also with BJP Minority Morcha staging demonstration demanding that police immediately arrest the guilty and punish the school management for not taking prompt action.
Facing the heat, Auradkar earlier in the day addressed the protesters, assuring them that action will be taken against the guilty and school management for alleged "inaction".
"We have solved blind cases in the recent past and will crack the Vibgyor School rape case as well," Auradkar said.
The opposition parties also have attacked the government over a string of rape incidents and demanded resignation of Home Minister K J George.
The Bangalore Police on Wednesday arrested Rustom Kerawalla, the Chairman of a Bangalore school in which a six-year-old girl was raped. He has been arrested under Section 201 of IPC which is destruction of evidence and Section 23 of Juvenile Justice Act. He has been arrested from Daman and Diu. He failed to ensure safety for child and refused to share information, Bangalore Police Commissioner MN Reddi said.
This is the second arrest in the case just days after a skating instructor of the school was arrested for committing the heinous crime.
A paedophile skating instructor arrested on Sunday for the rape of a six-year-old girl in an east Bangalore school allegedly tried to abuse at least four other children in the past three years. There are also doubts if he was using photos of his victims for pornography.
"We have reliable information that he used to click photographs of children and would also show them obscene videos of children in the Whitefield school (where he worked before 2011)," police commissioner Raghavendra H Auradkar said after announcing the arrest of Mustafa alias Munna, 30 from the religion of peace.