The court's order came as it heard a petition filed by accused Ashwani, a self-claimed medical practitioner, demanding an investigation into the role of the three.
According to a charge sheet filed in the case, Ashwani used to visit the shelter home to allegedly administer sedative-laced injections to the inmates before they were subjected to sexual abuse.
The Muzaffarpur horror came to light in May 2018 when the Bihar Social Welfare Department filed an FIR based on a social audit of the shelter home conducted by the Tata Institute of Social Sciences, Mumbai.
Brajesh Thakur, a journalist-turned-social activist heading the NGO which ran the shelter home, and other accused were arrested. The matter was handed over to the CBI in July last year.
State Social Welfare Minister Manju Verma was forced to resign after the opposition protests over reports that her husband and former Janata Dal-United legislator Chandreshwar Verma allegedly had close links with Thakur.
Thakur has been shifted to a jail in high-security Patiala following a Supreme Court order while other accused, including his close aides and some government officials, are lodged in jails at Patna and Muzaffarpur.
The trial of the case was this month shifted to Delhi.
The apex court had recently also directed the CBI to take over the probe into allegations of sexual abuse at all such shelter homes across the state.
Rashtriya Janata Dal spokesperson Bhai Virender demanded resignation of Nitish Kumar following the court order. "Nitish Kumar was involved in the case and was protecting the accused and trying to suppress the facts since the beginning," he said.