"The court has framed charges against Rajan under various charges of MCOCA; section 302 (murder) and 120-b (criminal conspiracy) of Indian Penal Code," said a CBI official.
After Special Judge Samir Adkar explained the charges to Mr Rajan, he pleaded not guilty. The court then posted the matter for September 7.
The framing of charges against Mr Rajan paves the way for the trial, five years after the veteran investigative journalist was shot dead in suburban Powai in 2011.
Chhota Rajan, currently lodged at high-security Tihar jail, was produced before the judge through video-conference.
Earlier this month on August 5, the central probe agency had filed a supplementary charge sheet against the gangster claiming he had the journalist murdered because Mr Dey's articles and a planned book portrayed Mr Rajan as 'chindi' (a small fry).
According to the CBI, Mr Rajan told one Manoj on phone that journalist Jigna Vora, a co-accused in the case, used to tell him "repeatedly" that Mr Dey "is writing wrong things and is in touch with the other gang and was a traitor."
Mr Dey's wife told CBI that for a month before his murder, he was very upset and he told her that he was going to die but not due to illness.
Mr Dey had planned a book, titled 'Chindi-Rags to Riches', wherein he was going to write the stories of 20 gangsters with humble origins.