The bench directed the CBI to submit all the materials collected in connection with the investigation before the court on the next date, in a sealed cover.
The bench said that considering the social ramifications of the gruesome incident, a three-member SIT would look into charges of evidence destruction and allegations made by the medic's parents.
The government order said the sanction was granted after "fully and carefully examining" case materials and records, including the FIR and related documents.
While addressing a rally in the run-up to polls, PM Modi had said files related to the RG Kar case would be reopened if the BJP comes to power in West Bengal.
CM Suvendu Adhikari said besides the suspensions of the three IPS officers, the role of the former CM Mamata Banerjee in connection with the incident will also be brought under the investigations.