The Home Ministry report now claims that P Chidambaram did not act alone in modifying the affidavit given to court.
A three-month search has failed to exhume crucial documents that were supposed to lay bare how the previous Congress-led government changed its stand on whether Ishrat Jehan, a 19-year-old college student killed in Gujarat, was a terrorist.
Five documents were identified by the government in March as key to proving that as Home Minister in 2009, P Chidambaram of the Congress misled a court in Gujarat by a complete switcharoo on whether Ishrat and the three men killed with her on a highway in 2004 were members of the Pakistan-based Lashkar-e-Taiba (LET) on a mission to kill then Gujarat Chief Minister Narendra Modi.
First, the Home Ministry told a court in July 2009 that the group was a terrorist cell. Two months later, the affidavit was changed to remove references to the Lashkar.
The ruling BJP has long held that deleting the Lashkar link was the Congress' conspiracy to undermine the threat to Mr Modi as well as to embarrass his government by claiming that Ishrat was killed in cold blood in a staged encounter by the Gujarat police.
The five missing documents include the letter written by the Home Secretary to the Attorney General and then the Attorney General' draft and then further amendment by the Home Minister and the final copy of the second affidavit.
The 50-page report prepared by the Home Ministry now claims that Mr Chidambaram did not act alone in modifying the affidavit given to court. It finds that as Home Secretary, GK Pillai was party to Mr Chidambaram's changes to the document, and that a search conducted of the files in the office used by Mr Pilliai reveals a note discussing the amendment, written by him and addressed to then Attorney General GE Vahanvati.
The same letter mentions a meeting on the affidavit that was attended by Law Minister Veerappa Moily, the Attorney General and the Home Secretary.
However, the official dossier on the Ishrat Jahan shooting does not include this letter - so either it was never placed on record, or it was not "the final letter", according to the new report.
Mr Moily has earlier told NDTV he had no recollection of any intervention in the Ishrat Jahan case.
The new Home Ministry report, however, steers clear of blaming anyone for manipulating documents, except for a reference to Dipti Vilasa, who was a joint secretary at the time in Mr Chidambaram's department.
The report notes how Mr Vilasa noticed some missing papers in 2009 itself and states he
"should have questioned the absence" of those papers and that it is "not customary of a joint secretary to accept a file which is not complete" in all respects".