"The court has framed charges under MCOCA against Rajan and he has pleaded innocence," said a CBI official.
Rajan, currently lodged at high-security Tihar jail, was produced before MCOCA judge Samir Adkar through video- conference.
On August 5, the central probe agency had filed a supplementary charge sheet against the gangster claiming that he had the journalist murdered because Dey's articles and a planned book portrayed Rajan as 'chindi' (a small fry).
"Dey was going to expose the fake patriotic mask used by him (Rajan) to secure himself and to accumulate wealth for his family. The book was to have that Rajan had no concern for those who made him big," the charge sheet had said.
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The book was also to portray Dawood Ibrahim, Rajan's friend-turned-foe, as being superior to him.
According to the charge sheet, Rajan, who was reportedly hiding in Malaysia, had called Dey for a meeting but the journalist refused, CBI said.
Last month, adjourning the hearing in the case, the MCOCA court had said it would go ahead with framing of charges as per the charge sheet earlier filed by Mumbai police's crime branch if the CBI failed to do so by August 5.
However, the agency stepped up and filed a 300-page charge sheet on the day.
Rajan was arrested at Bali airport in Indonesia on October 25 last year and deported to India. He is facing around 70 cases in Maharashtra, all now handed over to CBI.
The first charge sheet filed in the case in 2011 names Satiah Kaliya, Abhijeet Shinde, Arun Dake, Sachin Gaikwad, Anil Waghmode, Nilesh Shendge, Mangesh Agawane, Vinod Asrani, Paulson Joseph and Deepak Sisodia (all arrested).
Another charge sheet was filed against Vora the next year. She is accused of instigating Rajan against Dey owing to her own professional rivalry.