The body of the minor girl, who went missing this morning was recovered in a garbage dump in Nagla Kalar area here, police said.
The victim's family has alleged that she was strangled to death after being sexually assaulted, they said.
Hundreds of protesters gathered at Banna devi police station here and pelted stones following which police resorted to lathicharge to disperse the crowd, they said.
Alleging police inaction the crowd also blocked traffic for several hours on the main Aligarh-Delhi Grand Trunk road, they said.
When asked about reports of police firing in the air to disperse the mob, DIG Aligarh division Prakash D said that these reports were not true.
He said that there were no serious injuries to any one during the brick batting and subsequent lathicharge by the police.
The allegation of rape would only be confirmed after a post mortem is conducted, Prakash said, adding that the matter is being probed.