Union Home Secretary Rajiv Mehrishi is believed to have told Additional Secretary in the home ministry B K Prasad to speed up the probe and file a report at the earliest as the government may have to face queries of MPs in the coming session of Parliament beginning Monday, official sources said.
Top home ministry officials are of the opinion that the files were misplaced and could be found if a concerted effort is made.
Prasad, a Tamil Nadu cadre IAS officer, is retiring on May 31 and the government wants the task given to him to be completed as early as possible.
Government does not want any delay in finding the files and wants a quick report and Prasad has been told this in clear terms, the sources said.
The panel, constituted on March 14 following an uproar in Parliament, was asked to inquire into the circumstances in which the files related to the case of Ishrat Jahan, who was killed in an alleged fake encounter in Gujarat in 2004, went missing.
The panel was asked to find out the person responsible for keeping the files and relevant issues.
The papers which went missing from the home ministry include the copy of an affidavit vetted by the Attorney General and submitted in the Gujarat High Court in 2009 and the draft of the second affidavit vetted by the AG on which changes were made.
Two letters written by the then Home Secretary G K Pillai to the then Attorney General late G E Vahanvati and the copy of the draft affidavit have so far been untraceable.
Home Minister Rajnath Singh had disclosed in Parliament on March 10 that the files were missing.
The first affidavit was filed on the basis of inputs from Maharashtra and Gujarat Police besides the Intelligence Bureau where it was said 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, claimed to have been drafted by the then Home Minister P Chidambaram, said there was no conclusive evidence to prove that Ishrat was a terrorist, the officials said.
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.
Subsequently, Chidambaram had said Pillai is equally responsible for the change in affidavit.
Ishrat, Javed Shaikh alias Pranesh Pillai, Amjadali Akbarali Rana and Zeeshan Johar were killed in an encounter with Gujarat Police on the outskirts of Ahmedabad on June 15, 2004.
The Gujarat Police had then said those killed in the encounters were LeT terrorists and had landed in Gujarat to kill the then Chief Minister Narendra Modi.