New Delhi: Home Minister Rajnath Singh on Monday ordered an "internal inquiry" to probe how files concerning the affidavits filed in the Ishrat Jahan case have gone missing, said informed sources. The probe team, headed by Additional Secretary, Home, B. K. Prasad, will try to find out how the files concerning the "draft of the second affidavit" filed in the case went missing. "The internal probe will also probe the entire chain of file movements in the home ministry in 2009," a source told IANS. Last week, Rajnath Singh had announced in the Lok Sabha that an internal inquiry will be done in this regard. The Bharatiya Janata Party (BJP) and home ministry officials had alleged recently that the UPA government did a flip flop over the controversial 2004 shootout in which Ishrat, then a student of a Mumbai college and allegedly a Lashkar-e-Taiba operative, was killed. R.V.S. Mani, a former under secretary in the ministry, had told the media that he was pressurised to file the second or revised affidavit in the Supreme Court as against the first affidavit in which Ishrat Jahan was named a LeT operative. The BJP had accused the Congress regime of dropping Ishrat Jahan's name in order to malign the then Gujarat government when Narendra Modi was the chief minister. Former home secretary G.K. Pillai had also claimed that there was "political interference" in the case which led to the deletion of reference to LeT from the revised affidavit filed in 2009. On March 10, the home minister had told the Lok Sabha that "two letters from the then home secretary to the attorney general in 2009 have gone missing. The then attorney general had vetted two affidavits regarding the case. Those are also not available". Singh had said that the government has launched an "internal inquiry" to find the missing documents "which will bring all the facts out" in the open.