"I do not think that is correct. I do not think any important file could go missing when Chidambaram was the Home Minister. He was a very hands-on minister," senior spokesman Ajay Maken told reporters.
At that time, Maken was the deputy of Chidambaram in the Home Ministry but was not looking after the Internal Security division to which the file belonged.
Reports earlier had it that the one-man inquiry panel probing the missing files related to the case has concluded that the papers were "removed knowingly or unknowingly or misplaced" in September, 2009.
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.
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.