Sanjay Saxena, joint commissioner of police (crime), confirmed tonight that the crime branch had taken over the case from Nagpada police station.
Mukerjea, who is 'accused no 1' in this case, instigated other inmates to rioting after the death of a convict, the police had claimed earlier.
The 44-year-old former media executive was among the nearly 200 inmates of the Byculla Jail booked by the Nagpada police for rioting and other offences after they staged a protest over the death of convict Manju Govind Shette.
The next day, enraged women inmates rose in protest, some of them went up to the prison's roof, while others made a bonfire of newspapers and documents on the premises to express their anger, a police official said.
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The inmates alleged that Shette was mercilessly beaten up by the woman prison official which led to her death.
Indrani instigated the inmates, police had claimed.
Six jail personnel were suspended in connection with Shette's death. They were arrested yesterday on the charge of murder.
Indrani, her former husband Sanjeev Khanna and ex-driver Shyamvar Rai are accused of killing 24-year-old Sheena, Indrani's daughter from an earlier relationship, on April 24, 2012.