Five people, reportedly, abducted the girl last week when she was on her way to attend a relative's marriage ceremony.
As many as 578 rape cases were reported up to April 15, against 563 in 2017 during the same period, police said.
Mr. Thakur and Chatra Deputy Commissioner Jitendra Singh, along with senior police officials, visited Raja Kendua village under the Ithkhori police station to probe the incident on Saturday.
The unofficial ruling body fined the two men 50,000 rupees (£550) and ordered them to do 100 sit-ups.
One of the rape accused Ghannu Bhuiyyan, and his aides set the girl's house on fire as she was inside.
The girl's family members, however, alleged that the accused had set the girl on fire.
In another gruesome case that has rocked the country, 18 men are wanted over the death of a 16-year-old girl in the hill state of Jharkhand.
The victim returned home on Thursday and informed her family members.More news: National Football League players' union files grievance against Bengals in support of Eric Reid
The four accused of rape and murder have been booked under the Protection of Children from Sexual Offences Act (POCSO) Act, while Devi and Rajak were booked on charges of passing unlawful orders and tampering with evidence, according to Hindustan Times.
The main suspect and 14 others have already been arrested in connection with the earlier rape and burning case in the state.
Raghubar Das, the chief minister of the state of Jharkhand, tweeted that he was heartbroken by the incident.
The incidents come less than a month after India approved the death penalty for the rape of girls younger than 12, and increased the prison term for the rape of older girls and women.
Amid mounting outrage, the government has changed the law to allow execution for child rapists - but daily sexual assaults continue to be reported.
In India, rape has become a menace and such horrific incidents keep coming forward way too frequently.
Some 40,000 rape cases were reported in India in 2016, with many more believed to have gone unreported because of stigma attached to sex crimes in the country.