The group, Kerala Cyber Warriors, said the websites were hacked as a "tribute" to the young boy found with his throat slit in the school's washroom.
Visitors to at least four websites of the Ryan group were greeted with a black background and Pradyuman's photograph, with a title "Tribute to Pradyuman Thakur". "You may be gone. But you will never be forgotten," a message that the hacker group left behind said.
The group also criticised the Mumbai-headquartered Ryan management for failing to carry out background check of its employees, allowing the bus driver and conductor into the school buildings, non-functional CCTV cameras and allowing people other than students to share its washrooms.
Apart from the conductor of the institution's bus, two school officials including the school's human resources head have already been arrested but the Haryana police is also looking into the role by the school's top management.
In his application, Mr Thakur opposed the bail for the top officials for "the unpardonable, unprovoked, hellish cruel homicide" on the school campus.
Kerala Cyber Warriors, the group that calls itself ethical hackers, has targeted numerous Pakistani websites in the past too. The group also hacks Facebook groups and profiles that upload pornographic content.