Shette died here on June 23 after allegedly being beaten up by jail officials.
"We have submitted the charge sheet in magistrate's court," said a Crime Branch official.
The 990-page charge sheet contains statements of 182 witnesses, including Indrani Mukerjea, prime accused in the Sheena Bora murder case, who is lodged in the same prison, and 89 other jail inmates, he said.
The police have pressed charges of murder, destruction of evidence, criminal conspiracy and criminal intimidation against the accused.
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Prison officials Manisha Pokharkar (jailer), Wasima Sheikh, Sheetal Shegokar, Bindu Naikode, Surekha Gulwe and Aarti Shingne were arrested in the case following Shette's death at the J J Hospital here.
Footage of a CCTV inside the jail will also be submitted to the court as evidence, the police official said.
The prosecution today told the magistrate that they are presenting the charge sheet on the 88th day of the arrest of the six accused. As per the law, in murder cases the first charge sheet has to be filed within 90 days of arrest.
Indrani Mukerjea, in her complaint to police against Byculla Jail officials, had said that she and others saw Shette being beaten up.
She herself was beaten up and threatened of sexual assault by officials for coming forward to submit complaint over Shette's death and record statement before a magistrate, Indrani alleged.
Jail inmates had staged a violent protest after the 45- year-old Manjula Shette, serving a life sentence, died.
Jail officials allegedly beat up Shette brutally when she, as a warden, failed to account for 'two eggs and five loaves of bread' which were to be distributed to other prisoners.