The prosecution filed the charge sheet against Jan before the court of Chief Judicial Magistrate Srinagar.
Jan was arrested on August 15, 2010 after he hurled a shoe towards the Chief Minister soon after the latter unfurled the national tricolour.
The cop was granted the wish to meet the Chief Minister next day, who directed that the legal proceedings against him be dropped as he had apologised for the act.
The court sent the accused to judicial custody as he is also facing charges of extorting money from a truck driver in Pampore area of Pulwama district last week.
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Police had asked the Law Department if there was any written order regarding the pardon.
Jan, who was a head constable in the police force before being dismissed on disciplinary grounds, was arrested on May 14 after he allegedly extorted an amount of Rs 38,000 from a truck driver Kulvinder Singh, of Punjab, in Pampore area of Pulwama.