The Supreme Court on Monday directed the Central Bureau of Investigation to complete its investigation in the Muzaffarpur shelter home rape case within three months, ANI reported. The agency had approached the court seeking six months to complete the inquiry.

A vacation bench comprising Justices Indu Malhotra and MR Shah directed the agency to investigate allegations of unnatural sexual assault under Section 377 of the Indian Penal Code, and allegations of assault on the children being recorded, PTI reported. The court was hearing a petition that alleged the CBI had not carried out the investigation properly.

The court also asked the investigative agency to conduct inquiries into the role of outsiders who allegedly facilitated the sexual assault of inmates by administering them intoxicants.

The court said all other agencies involved in the case should cooperate with the CBI inquiry. It dismissed an intervention petition filed by prime accused Brajesh Thakur.

Additional Solicitor General Madhavi Divan, appearing for the CBI, told the court that the agency has so far excavated two bodies. Divan said the agency was waiting for the forensic report to determine the identities of the bodies. She added that the trial against 21 accused was progressing well.

Advocates Shekhar Naphade and Fauzia Shakil, representing the petitioner, said the allegations of trafficking have not been investigated properly.

“How many girls are missing [from the shelter home]?” the court asked the CBI. Divan, in response, said there were 471 inmates, and 11 girls were murdered, but there were difficulties ascertaining their identities. She claimed that four girls died of “natural causes”.

The alleged sexual exploitation of children at the shelter came to light in April 2018 after Mumbai’s Tata Institute of Social Sciences submitted an audit report of 110 shelter homes in Bihar. The audit was ordered by the state government, which filed a first information report against 11 people on May 31.

At least 34 inmates were allegedly drugged and raped, according to law enforcement agencies. The Central Bureau of Investigation – in its chargesheet filed in December – alleged that Brajesh Thakur had coerced girls to dance to vulgar songs and have sexual intercourse with guests. Thakur is currently lodged in a high-security prison in Punjab.

Seven girls, including five witnesses in the case, went missing from a government-run children’s home in Mokama town in February. The inmates were shifted to the Children’s Home for Girls in Mokama’s Nazareth Hospital from Muzaffarpur a few months back.