The child went missing on September 9 from her house. Her body was later found in the house of her neighbour Raju.
The case was registered against Usman, a native of Adhur, under the Section 12 of POCSO Act and Section 75 of the Juvenile Justice Act, days after the 12-year-old girl died by suicide.
The National Eligibility cum Entrance Test (NEET) Undergraduate, 2021, was held on Sunday.
Relatives had found the husband, wife and their three-year-old son dead inside their house.
According to the police, the man had come to the house after Savita threatened to kill herself over the phone.
The deceased was identified as Kavya Mohan, daughter of Mohan and Seena.
The driver, identified as Rajeevan of Chanthiroor in Aroor, has died. He was 45 years old.
Vishnu, 32, of Chengamanad, who was reportedly depressed by the death of his dear ones, had returned to Kerala on August 5.
According to the police, Vijay, 38, owner of Nandanam Hotel in Peerumade, was found hanging on Tuesday.
Vishnu Bhaskar of Manganam Painkulathu House, who was a bachelor, was employed in South Indian Bank, Kozhencherry.