A civic official said the demolition work on Monday was incomplete and the actor had been asked to shift an illegal prayer (pooja) room, failing which it would be razed.
Mr Sinha will now be booked under BMC laws for the unauthorized constructions and the civic body will also recover the demolition costs from him.
The Sinhas have been living since 2012 in this redeveloped residence in the fashionable Juhu area of western suburbs.
The civic officials found in Mr Sinha's home an illegal toilet on the terrace, two more toilets and a small pantry in the refuge area, an office and a prayer room in the stilt area - which the actor has described as "minor alterations" but did not protest at their removal.
The BMC had earlier slapped Mr Sinha with notices under the Maharashtra Region & Town Planning Act (MRTP) for the illegal constructions on December 6 but they were ignored, though the actor claimed he was awaiting permission for additional construction rights for the same.
The BMC's approved plans for the structure included stilts, a double-floor podium and an eight-storey building above, but the alleged illegalities are believed to have come up after the family shifted in the redeveloped premises five years ago.
Besides Mr Sinha, several other Bollywood personalities, including Shah Rukh Khan and Kapil Sharma, have faced the BMC demolition squads.
Others like Amitabh Bachchan and Rajkumar Hirani were served notices for alleged violations at their Goregaon bungalows in October 2017.