Sharma informed the court that an FIR under Section 377 IPC (unnatural offences) and the Protection of Children from Sexual Offences Act has been registered.
The boy was brought to the home by an NGO three years ago after his mother died of AIDS. His stepfather was lodged in Tihar for raping his daughter.
The police said medical tests on the three suspects showed that "they were innocent" - they didn't test positive for HIV.
The police said the Child Welfare Committee had already shifted the boy to Asha Kiran home in Rohini.
Bharti Ali of the Haq Centre for Child Rights told HT: "The incident happened nearly 20 days ago. What will medical test of the suspects prove now? The CWC should have acted fast."