17 people have been booked for three of the alleged rapes
Media reported that the women from the Fugana and Shamli villages in the district, have alleged that they were gang-raped by rioters during the communal clashes three weeks ago.
Some women, who are married and in their early 40s, also alleged that they knew their attackers, who gang-raped them before burning down their homes in the first two days of the violence.
The police are investigating the complaints. 17 people have been booked for three of the alleged rapes.
"There are five complaints which are under investigation. We are probing it in the most impartial way and we will take action," said Harinarayan Singh, a senior Muzaffarnagar police officer.
Fugana was one of the villages worst hit by the clashes that erupted in the aftermath of the killing of three men in August, two Jats and one Muslim boy. The violence spiraled as incendiary speeches by politicians and rumours fed the simmering tension between two communities.
Three MLAs were arrested and half a dozen others have been booked for inciting the violence.
Thousands of families living in relief camps have refused to go back to their villages out of fear. Many of them said they saw their relatives attacked and killed by their own neighbours.