The decision comes after the agency received a legal advice suggesting that the case may be categorised as the "rarest of rare", deserving capital punishment, according to officials.
Former principal of RG Kar Medical College and Hospital Sandip Ghosh former officer in charge of the Tala police station Abhijit Mondal were the two main accused.
During the hearing, the National Task Force (NTF), formed to create a protocol for the safety of health professionals, submitted its report in the apex court.
The court observed that the CBI report indicated that the agency was probing the role of other persons as a part of its ongoing investigation and sought a further status report within three weeks.