The two accused, Gaurav and Amardeep, were arrested yesterday while appearing for a written exam at the police recruitment centres, said SP (Rural) Alok Priyadarshi.
Reportedly the accused had already appeared for their physical tests before they were arrested, he added.
The duo, who were produced in a court today, have been sent to judicial custody till December 23.
According to SIT sources, attachment proceedings against the two have been initiated by court in connection with the cases.
More than 60 people were killed and 40,000 displaced during riots in Muzaffarnagar district and its adjoining areas in September 2013.