New Delhi: Union Home Minister Rajnath Singh on Monday constituted a high-level team to probe how some important files related to the alleged fake encounter of Ishrat Jahan went missing.


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According to media reports, Additional Home Secretary will head the probe.


Rajnath Singh had last week told Lok Sabha that many documents related to the preparation of the MHA's second affidavit in the Ishrat Jahan encounter case were missing and an internal inquiry had been ordered.


Replying to a motion on the change in the Ishrat case affidavit, filed in the Gujarat High Court on September 29, 2009, the Home Minister said the Ministry is conducting an internal inquiry on missing documents from the Ishrat affidavit file.


The minister said two letters written by the then home secretary (GK Pillai) to the Attorney General (AG) are not traceable. The draft of the second affidavit that came from the AG in which the then home minister (P Chidambaram) made changes is also missing.


Singh also accused the erstwhile UPA government of hatching a “deep conspiracy” to frame Narendra Modi when he was the Gujarat Chief Minister.


Singh also alleged that the previous regime had done a ‘flip-flop’ on the links of Ishrat Jahan with terror outfit LeT


On June 15, 2004, the Gujarat Police shot dead three men and a woman – 19-year-old Ishrat Jahan –while they were allegedly on a Lashkar mission to assassinate then Gujarat chief minister Narendra Modi.


However, a probe conducted by the Central Bureau of Investigation (CBI) and a high court-appointed Special Investigation Team found it to be a “fake encounter”.


The first affidavit in the case was filed on the basis of inputs from Maharashtra and Gujarat Police besides the Intelligence Bureau where it was said that the 19-year-old girl from Mumbai outskirts was a Lashkar-e-Taiba activist but it was ignored in the second affidavit, Home Ministry officials said.


The second affidavit, believed to have been drafted by the then Home Minister P Chidambaram, said there was no conclusive evidence to prove that Ishrat was a terrorist.


Former Union Home Secretary G K Pillai had claimed that as Home Minister, Chidambaram had recalled the file a month after the original affidavit, which described Ishrat and her slain aides as LeT operatives, was filed in the court.