New Delhi: Citing a newspaper report suggesing the officer investigating missing files in the controversial Ishrat Jahan encounter case “tutored” a witness, former Home Minister P. Chidambaram on Thursday said his stand on the issue has finally been vindicated.

Chidambaram, who had earlier drawn flak for allegedly amending an affidavit filed by the central government in the Ishrat case, accused the Narendra Modi government of creating a “fake controversy” over two affidavits filed in the matter and preparing a “doctored” report on the missing files.

On Wednesday, Home Ministry Additional Secretary B.K. Prasad submitted his inquiry report on the missing files.

However, according to The Indian Express daily, Prasad was recorded over the phone telling a witness, officer Ashok Kumar, the questions he would ask and also suggesting answers.

“The newspaper report completely vindicates the position that I had taken on the two affidavits. The first affidavit of August 6, 2009 disclosed the intelligence inputs that had been shared by the Central government with the state government,” Chidambaram told reporters here on Thursday.

“The first affidavit was misinterpreted and misused to defend the encounter. It was, therefore, necessary to clarify the first affidavit. Hence, a further affidavit was filed on September 29, 2009 clarifying that intelligence inputs do not constitute conclusive proof and it is for the state government and the state police to act on such inputs.”

Chidambaram said the contents of the ‘further affidavit’ were absolutely clear and correct.

“It is unfortunate that most people who commented on the matter had not cared to read the further affidavit. The sequence of events conclusively establishes that we had acted in a totally transparent manner. The draft of the further affidavit was vetted by the Attorney General, the highest law officer of the country, before it was filed,” Chidambaram said.

“The moral of the story is that even a doctored report of the Inquiry Officer cannot hide the truth. The real issue is whether Ishrat Jahan and three others were killed in a genuine encounter or a fake encounter. Only the trial of the case, pending since July 2013, will bring out the truth,” he added.

Reacting to the issue, Minister of State for Parliamentary Affairs Mukhtar Abbas Naqvi said on Thursday that the missing documents of the Ishrat case amounted to “anti-national activity.”

“It is a serious matter which definitely and clearly indicates an anti-national activity and conspiracy. Those involved in this will be punished,” he said here.

According to sources in the Home Ministry, Prasad’s inquiry establishes that documents on the 2004 killing of 19-year-old college student Ishrat and three others by the Gujarat police had indeed gone missing when Chidambaram was Home Minister.

The ruling Bharatiya Janata Party (BJP) had earlier alleged that the missing files indicated a cover-up at a time the Congress-led government amended its own court documents and came out with a new one removing all references to Ishrat’s alleged connection with terrorist outfit Lashkar-e-Taiba, to suit the party’s stand that an innocent student had been shot dead on the orders of Gujarat government.

BJP even accused Congress president Sonia Gandhi, Congress vice-president Rahul Gandhi and Chidambaram of plotting a conspiracy to discredit and frame Modi by distorting facts about Ishrat. On its part, Congress accused Modi and BJP chief Amit Shah of attempting to derail the judicial process and trial in the case.

Ashok Kumar, then a director and now a joint secretary, told Prasad during his deposition that he was on tour when the decision to file the second affadivit was taken and he had “during my entire tenure neither dealt with this case nor kept this file in my custody.”

Meanwhile, Prasad said in a statement Thursday, “the questions which have been quoted from my alleged conversation by Indian Express were never asked from Ashok Kumar and the answers which are quoted by newspaper were never given by him.”

Prasad has reported to the Home Ministry that the documents were “removed knowingly or unknowingly, or misplaced” in 2009 when Chidambaram was the home minister. He said he had conducted a free and fair inquiry which his inquiry report will reveal.

“All officers enquired by me are or have been senior officers in the government and are fully capable of answering questions relating to the probe on their own and there is no question of the alleged tutoring,” Prasad said in the statement.

Earlier in March, former Home Secretary GK Pillai and former undersecretary in the ministry RVS Mani said the reference to Ishrat’s Lashkar links were present in the first affidavit but was removed in a second affidavit on the directions of Chidambaram.