New Delhi Home Minister Rajnath Singh on Thursday said key documents related to the Ishrat Jahan case have gone missing and accused the previous Congress-led government of a flip-flop over the controversial 2004 shootout that killed the alleged Lashkar-e-Taiba woman operative. "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," Rajnath Singh told the Lok Sabha on Thursday, replying to a brief debate on the controversial June 15, 2004, shootout. He said that the government has launched an "internal inquiry" to find the missing documents "which will bring all the facts out" in the open. Without naming Congress's P. Chidambaram, Rajnath Singh alleged that affidavits regarding the case were corrected on the intervention of the then home minister and reaffirmed that an investigation has found that the Thane girl was a terrorist -- a claim also seconded by American-Pakistani terrorist David Coleman Headley in his deposition. "I am pained to say that there was a flip-flop on Ishrat Jahan case during the previous UPA (United Progressive Alliance) government," Rajnath Singh said, amid a pandemonium by some opposition members. "She was described as an LeT terrorist in the first affidavit filed in the Gujarat High Court but unfortunately the facts were given another dimension in an additional affidavit which was filed a month later. It seems an attempt was made to weaken the case." The minister also accused the previous government of hatching a conspiracy to malign the then Gujarat chief minister Narendra Modi and his government. "The affidavit was changed to malign the Gujarat government, the then chief minister. A conspiracy was hatched to drag him into the case." Rajnath Singh said that government was not relying solely on the testimony of Headley - a Lashkar operative who scouted terror targets before the 2008 Mumbai terror attack. Headley is currently in a US jail from where he was questioned by an Indian magistrate last month through videoconferencing. The Pakistani-American terrorist said he had heard his LeT handlers talk about a girl in India named Ishrat. The controversy over the case flared up again after Headley made the startling claim on February 11 this year about the 2004 Gujarat encounter -- the already murky Ishrat Jahan case has become even murkier. Rajnath Singh alleged that the previous government had tried to give a political and communal colour to terrorism in India and reminded the Congress of the "saffron terror" label given to describe acts of violence allegedly committed by Hindu nationalists. "Saffron terror was the previous government's term. Colour, creed and religion are not linked to terrorism. They gave a communal colour to terrorism. This is opportunistic secularism." He said that the whole world was battling "the menace of terrorism" and "there should not be politics over it"