Sanjoy Roy, 33, the lone accused in the case, pleaded not guilty before the judge in a closed court on Friday in Kolkata, his lawyer Sourav Bandyopadhyay told AFP.
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.
Reacting to the development, the Left parties and the Congress on Saturday took out protest rallies at various locations in Kolkata, alleging that the CBI has "failed" to deliver justice in the case.
A Kolkata court granted bail to ex-RG Kar Medical College principal Sandip Ghosh and former Tala police station officer Abhijit Mondal in the rape and murder case of an on-duty doctor at the hospital.