He said that the CBI registered separate cases against Bhagalpur-based Boys' Children Home run by Rupam Pragati Samaj Samiti and House Mother of Children Home in Gaya on the basis of FIRs registered by the Bihar Police last year.
The action comes almost one-and-half month after the Supreme Court directed the investigation agency to probe alleged abuse of inmates at 17 shelter homes listed in a Tata Institute of Social Sciences (TISS)'s study report.
In the FIR against the Gaya shelter home, the CBI has cited the TISS report, which highlights that the House Mother of Children Home, Gaya ill-treated children by using abusive language, physical assault, forcing them to write lewd messages and taking manual labour.
"There were no proper arrangements for medical treatment, study, recreation and food for the minor inmates at the shelter home," it said.
On the TISS report on Bhagalpur shelter home, it alleged that the director and other officials were running Boys' Children Home in violation of provisions of the Juvenile Justice Act and committed financial irregularities.
It also said that boys were mentally and physically abused there. There were no educational recreational or vocational facilities available in the children home for the inmates.
The official said that the observations in the TISS report have been included in the FIR to serve as primary allegations.
The crime against minors came to light following a social audit by TISS, Mumbai, over six months ago. The Supreme Court is monitoring the CBI probe.
The Muzaffarpur case caught national attention last year after the TISS study highlighted that out of the 42 girls lodged at the short-stay home run by an NGO, 34 were found to have sexually been assaulted. The shelter home was being run by Brajesh Pathak.
An FIR was lodged against 11 people, including Thakur, on May 31. The probe was later taken over by the CBI.