Varma had said in his petition the inquiry report that had cleared him in the case had been submitted to the high court.
However, the Gujarat high court registry and the state government have stated that the clean chit report has gone “missing”.
In 2012, Hiralal Shiyal, brother of Jasu Shiyal, who was killed in an encounter, filed a petition in the high court, seeking a fresh probe into the case.
The state government supported the petitioner after Verma began his probe into the Ishrat encounter case as a member of the Gujarat high court-appointed special investigation team, which was later dissolved.
Former under secretary in the ministry of home affairs RVS Mani had earlier alleged that Verma had coerced him into signing statements and also claimed the Mumbai and Parliament attacks were “orchestrated by the government in power”.