"We have registered an FIR and started the probe into Dr Sachan's alleged murder," a senior CBI official told PTI.
An FIR under sections 302 (murder) and 120B (conspiracy) had been lodged at Gosaiganj police station last month against unidentified persons on an application moved by Sachan's wife Malti. The CBI has re-registered this case and started the probe, he said.
The Allahabad High Court had directed the agency to complete the investigation into the case in three months.
Arrested on charges of embezzling National Rural Health Mission funds, 52-year-old Sachan was also named as the key conspirator in the murder of CMO B P Singh on April 2 following the June 17 arrest of three shooters hired to kill him.
Sachan's body was found with multiple injuries in the jail hospital toilet on June 22 night. The state government and police had initially claimed Sachan committed suicide but a judicial probe concluded that it was prima facie a case of murder.
The postmortem had revealed nine injury marks on the body including on the neck, elbows, wrists and thigh. Bowing to strident demands, UP Chief Minister Mayawati had on July 13 ordered a CBI inquiry into the death of Sachan.