The youth were arrested after the victim's father complained to Santhosh Kumar Singh, Jabalpur Superintendent of Police (SP) that Patan police failed to file his complaint despite repeated pleas.
The victim's father accused Rafiq and Danish of kidnapping his daughter a month back and repeatedly raping her for a month after drugging her.
The girl, who escaped from the clutches of the men, managed to reach her home and narrated the incident following which her father went to file an FIR with the police but in vain.
Senior police officials have now asked the Patan police to register a complaint and take action immediately. A probe into why a complaint was not registered has also been ordered.
A complaint would be registered against those who failed to act on time, said Singh.