According to the FIR, the minor was recently abducted by the trio from Basaira village and was taken to a nearby jungle where she was gangraped by them.
The accused had threatened to kill her if she revealed of the incident to anyone, police said.
They have been charged under Sections 376 (punishment for rape), 363 (punishment for kidnapping) and 506 (punishment for criminal intimidation) of the IPC.
Ahmed has denied the charges against his son and brother-in-law, saying it was a "political conspiracy" against him and they have been falsely implicated.
The girl has been sent for medical examination, police said, adding that none of the accused have been arrested.