Over 200 persons, including a few personnel, were injured during the nine-day agitation.
An official said the charges were in connection with an audio clip of Virender's conversation.
An FIR has been registered in Rohtak against Virender and Man Singh Dalal, who also allegedly figured in the taped conversation, under various sections of the IPC, including section 124-A (sedition) and section 120-B (conspiracy), Singhal told the media here.
They have also been charged with IPC sections 153-A (promoting enmity between classes) and section 153-B (imputation, assertion prejudicial to national integration), he said.
The FIR against the duo has been registered on a complaint of a Bhiwani resident Pankaj Kumar, he said.
Virender had earlier accepted that the voice in the clip was his but alleged that it had been "doctored".
He has maintained that nowhere had he talked about instigating Jats or anyone. "Moreover, the conversation is an old one, much before the current unrest started," he had said.
"Twenty eight people have been killed during the stir. We have arrested 127 persons and registered FIR against 535 others. Over 200 persons including few security personnel were also injured during the agitation," Singhal said.
Curfew was lifted in Hisar district and relaxed in violence-hit Rohtak and Bhiwani districts while rail and road traffic were gradually resumed on routes which had remained blocked during the agitation.
A totalof 35 popular trains including Shri Mata Vaishno Devi Katra Mail, Kalka Shatabdi, Amritsar Shatabdi and Jammu Rajdhani resumed operation today while about services of 60 trains were still affected.
In Bhiwani, one of the worst-affected districts in the agitation, authorities gave a four-hour relaxation in curfew as the situation was improving, officials said.
Curfew was lifted from Hisar and its nearby town Hansi, though prohibitory orders under Section 144 banning assembly of five or more persons will remain in force.
Day-long relaxation in curfew was allowed in Rohtak, the epicentre of the pro quota agitation in Haryana.
"The situation is peaceful in Rohtak city today. No untoward incident has been reported from anywhere," a senior police official said.
Life was also returning to normal in violence-hit Sonipat, where three persons had died in a clash with security forces two days back.
Security forces were patrolling sensitive areas including Bhiwani, Hisar, Sonipat and Rohtak, officials said.
The arterial Delhi-Ambala National Highway, which had remained closed for four days, was thrown open last evening.
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