Baalu, the sole DMK representative in the 30-member Committee, is understood to have opposed the findings in the report and raised questions as to how it could come to conclusions when documents before various courts were not available for examination by the Committee.
Sources said in his 26-page dissent note, he is also believed to have said that the DoT affidavits submitted to the Supreme Court and the High Court have not been examined by the Committee.
In a recent letter to JPC Chairman P C Chacko, Baalu had demanded examining the documents available with the court and also calling officials who had prepared the affidavits.
He had been demanding calling Raja in person to depose before the panel.
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Raja had made a written deposition before the JPC in which he had claimed that all decisions taken by him were in consultation with Prime Minister Manmohan Singh.
In the July 27 meeting of the Committee, Baalu had again raised the issue of calling Raja and examining the fresh evidence before adopting the report.
"The Committee wish to point out that the procedure" regarding the First-Come-First-Served (FCFS) criteria was a "misrepresentation of facts and in tactic deviation from the existing procedure," it said.