"We have filed an FIR in the Ishrat Jahan missing documents case and are planning further proceedings," Deputy Commissioner of Police, New Delhi, Jatin Narwal said on Sunday.
An Under Secretary in the Home Ministry has filed the FIR at the Parliament Street Police station here under Section 409 (criminal breach of trust by public servants) of the Indian Penal Code.
The FIR seeks a probe on "why, how and under what circumstances" five documents related to the case went missing, sources said.
"The complaint from Home Ministry was filed on August 26 and a police case has been registered under 'stealing' category earlier this month on September 22," a source said here.
An official panel was appointed by the government to probe the "missing documents" after former Home Secretary G.K. Pillai sparked a row by claiming that some papers related to an affidavit in the case were changed by then Home Minister P. Chidambaram.
The Congress and Chidambaram had denied the charge and instead charged the Modi government with "politicising" the issue.
The Home Ministry had ordered the probe by senior IAS officer B.K. Prasad on March 14. He was also given extension in July amid complaints that he had tried to "tutor" some of the witnesses, including retired officials.
The ministry had maintained that since this is "highly sensitive enquiry" wherein allegations have come in that efforts were made to conceal the terror link of Ishrat Jahan, the government desired that the panel submit a "detailed and final report".
The NDA government has maintained that "the second affidavit", which was different from the original, had said there was no evidence to link Ishrat to the terror group.
According to sources in the Home Ministry, the papers which went missing and listed in the FIR are the office copy of the letter and enclosure sent by the then Home Secretary to the then Attorney General on September 18, 2009, a copy of another letter sent by then Home Secretary to the AG on September 18, 2009, and the draft of a further affidavit as vetted by the AG.
Ishrat Jahan and three others were killed in an alleged staged shootout in Gujarat in 2004. Police had claimed that they were Lashkar-e-Taiba militants on a mission to kill then Gujarat Chief Minister Narendra Modi.
The controversy over the case flared up after David Headley, a Lashkar operative involved in the 26/11 Mumbai attack, also made some observations on February 11 this year about the case.