The agency, which filed a status report in a sealed envelope before a bench of Justices G S Singhvi and A K Ganguly, said Raja will face charges of "cheating, forgery, and corruption".
It said Swan Telecom and Loop Telecom were allegedly used as front companies by Reliance Group and Essar respectively.
Essar already has stakes in Vodafone.
Swam Telecom's promoter Shahid Usman Balwa has been arrested by the CBI and ADAG firm RCom's Chairman Anil Ambani has also appeared before the agency in connection with the 2G spectrum scam.
The CBI submitted before the court that Swan and Loop hid the details about their companies to get spectrum and they will be facing charges of "cheating" and "criminal conspiracy".
The agency said there was evidence of "forgery" in altering of first-come-first-serve policy to allow some companies to get 2G spectrum during Raja's tenure as telecom minister.
It said the main charge sheet will be filed on April 2 against four individuals including Raja, some telecom honchos and two companies for their involvement in the 2G scam.
The CBI also said that the supplementary charge sheet will be filed by April 25 and investigation in the scam completed by May 31.
Senior advocate K K Venugopal, appearing for the CBI, placed a transcript of telephonic conversation of corporate lobbyist Niira Radia with top corporate honchos and politicians and said, "these telephonic records will be used as evidence in criminal prosecution of the accused in the scam".
The bench, after hearing his argument, said there is no need to file the draft charge sheet for approval as directed by it earlier as the CBI has assured the court that the charge sheet will definitely be filed on April 2.