Additional chief judicial magistrate Haradhan Mukhopadhyay incorporated the section on the ground that the Section had been inadvertantly dropped earlier.
CBI had moved the court seeking incorporation of Section 409 of IPC which allows a charge sheet to be filed against an accused within 90 days of arrest.
Mitra had last Friday filed a bail plea in the Alipore District and Sessions Judge's Court and it is scheduled to come up for hearing on February 11.
The bail petition was filed apparently to take advantage of the prosecution's failure to file the charge sheet within the statutory period of 60 days within which the prosecution would have to file the charge sheet under the Sections he was charged earlier.
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There was high drama in the court room today with a section of lawyers demanding that the defence lawyers be heard before passing any order.
They also told the court that as a senior lawyer died yesterday, they were not attending court as a mark of respect to the departed colleague and as such the judge should not pass any order in this matter.
Mukhopadhyay, however, remained firm and said that he would pass the order today itself.
Mitra is now being held in Alipore Correctional Home.
The district and sessions judge's court had granted bail to another accused in the Saradha scam, Srinjoy Bose, on the ground that even after completing 60 days in custody, no charge sheet was filed against him.