The report, on which six parties have submitted dissent notes, also rubbishes the loss figure of Rs 1.76 lakh crore estimated by CAG, saying it was "ill-conceived".
JPC Chairman P C Chacko submitted the report along with the dissent notes, which termed it as a "bundle of contradictions" to the Speaker at her official residence.
The report, which delved into the period between 1998 and 2009, will be tabled in Parliament in the Winter Session likely to commence in the first week of December.
The dissent notes are a way to record members' objections to the findings and are appended with the final report when it is tabled.
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Eleven opposition members, including BJP's 5 and one each of BJD, TMC, CPI, CPI(M), AIADMK and DMK voted against the JPC report. BJP's Gopinath Munde had not attended the meeting.
In its dissent note, BJP insisted that the Prime Minister and then Finance Minister P Chidambaram should have been asked to depose before the JPC.
The report, which was adopted by majority vote on September 27 in the absence of two JD(U) members, also accuses Raja of forging the press note of January 7, 2008, after it was seen by the then Solicitor General G E Vahanvati.
Besides Congress, its UPA ally NCP and outside supporters of the ruling alliance SP and BSP had supported the report.