The charge sheet was filed against Rajender Foji, Manga, Arvind, Sharan, Harmore, Azad, Mangeyram, Sahensarpal and Rajender Kumar last evening in the court of Chief Judicial Magistrate Narendra Kumar, police said today.
According to the prosecution, Amroz, Maherban and Ajmal were beaten to death by the accused at Mohamadpur Raisingh village under Budhana police station on October 30.
A case against 15 persons was registered by the police in connection with the incident and nine of them were arrested, while the remaining six are absconding, police said.
The SIT has completed investigation in 30 cases.
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Meanwhile, Senior Superintendent of Police, H N Singh said non-bailable arrest warrants have been issued against 147 absconding persons who failed to appear in the court.
Police has registered 534 cases against 6,423 persons in connection with the riots in the district.
Over 60 persons were killed and more than 40,000 displaced in communal violence in Muzaffarnagar and adjoining areas in September last year.