Union Home Secretary Rajiv Mehrishi is said to have told Additional Secretary in the Home Ministry B K Prasad to speed up the probe and submit his report by the end of this month.
Prasad, a Tamil Nadu cadre IAS officer, is retiring on May 31 and the government wants the task given to him to be completed before his service comes to an end, official sources said.
Top Home Ministry officials are of the opinion that the Ishrat-related files were misplaced and could be found if a concerted effort is made.
Government seems to be unhappy over the delay in finding the files and wants a quick report and Prasad has been told this in clear terms, the sources said.
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It 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.
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.
Ishrat, Javed Shaikh alias Pranesh Pillai, Amjadali Akbarali Rana and Zeeshan Johar were killed in the encounter with Gujarat Police on the outskirts of Ahmedabad on June 15, 2004.
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Meanwhile, official sources said the probe into the missing papers related to the Ishrat case has hit a roadblock at a time when the Ministry wants to finalise the inquiry findings by May 31.
While the one-man inquiry panel has met and spoken to most of crucial players of the period like Pillai and others, one key man continues to dodge the probe panel.
The panel has even given a written questionnaire to Diptivilasa but he has consistently refused to answer any queries on the issue.
Diptivilasa, who had retired from service in 2014, was Joint Secretary in the period when the second affidavit related to Ishrat Jahan was filed.