The order was passed by magistrate D S Patale.
The court asked the concerned deputy commissioner of police to conduct a probe and file a report.
According to advocate Vinod Gangwal, the complainant, he had approached the police to help a woman whose three years old daughter had been raped.
He alleges that initially the police at Kharghar refused to register the complaint, and later, although they registered an FIR in the rape case, another case was lodged against Gangwal and he was arrested.