Additional Chief Judicial Magistrate Ankur Sharma issued the non-bailable warrants and asked the accused to be present in court on June 22.
Bijnor MP Bhartendu Singh, Uttar Pradesh Minister Suresh Rana, and MLA Sangeet Som, were also accused in the case.
They too had not appeared in the court. The court had allowed their application seeking exemption from personal appearance in hearings, the prosecution said.
The accused had allegedly participated in a "mahapanchayat" and incited violence through their speeches in the last week of August, 2013.
The riots in Muzaffarnagar and adjoining areas in 2013 had led to 60 deaths and displaced 40,000 people.