Additional Chief Judicial Magistrate Sitaram issued bailable warrants against the two, directing them to appear before it on November 24 in connection with the case. The court order comes after the Union minister for agriculture and BJP MLA failed to appear before it again on Monday.
Earlier, a bailable warrant was issued by the court on October 23 against several accused in the Muzaffarnagar riots case including Balyan, BJP Member of Parliament Bhartendu Singh, Rana and Sadhvi Prachi.
However, the court has withdrawn the warrant against Singh after he surrendered before the court on Monday and submitted a personal bond of Rs 20,000 and an undertaking that he would appear in court on November 24.
According to the prosecution, they are charged with offences under Indian Penal Code sections 188 (violating prohibitory orders), 353 (assault or criminal force to deter public servant from discharging his duty) and 341 (wrongful restraint).
It is alleged that they participated in a Nadala Mador panchayat meeting and violated prohibitory orders and incited violence through their speeches on August 30, 2013.
As many as 60 persons were killed and over 40,000 people were displaced during the communal clashes in Muzaffarnagar and adjoining areas in August last year.