The court said that Rajan suspected that J Dey was working for Dawood Ibrahim and the journalist was showing him in a poor and weak position.
Vora and Paulson Joseph were acquitted due to lack of evidence.
The framing of charges against Rajan paves the way for the trial, five years after the veteran investigative journalist was shot dead in suburban Powai in 2011.
"The court has framed charges under MCOCA against Rajan and he has pleaded innocence," said a Central Bureau of Investigation official.