Six women had lodged complaints that they were gangraped during the clashes and their houses were burnt by the rioters, police said.
The rape victims were produced in the court and their statements were recorded, they said.
According to the local police, none of the accused has been arrested so far as they are absconding.
The National commission for minorities had expressed concern over delay in arrests of the accused in gangrape cases.
Meanwhile, two riot accused have been arrested and sent to 14 days judicial custody in connection with killings in Bahawdi village under Phugana police station.
Bhullar Singh and Rampal were produced in the court on Monday.
According to the prosecution, the duo was involved in murder and setting ablaze property during riots in the district on September 7, 2013.
The riots in Muzaffarnagar and adjoining areas last year claimed over 60 lives and left thousands homeless.