Kathua Superintendent of Police (SP) Suleman Choudhary has been replaced with Shridhar Patil.
The development comes days after the investigation began into the rape and murder of an eight-year-old girl from the district.
The case dates back to January when the father of the victim filed an FIR after the child went missing on January 10.
After an initial arrest, protests followed questioning the handling of the case by the local police. The case was then transferred to Jammu and Kashmir Police's Crime Branch, which filed a charge sheet earlier this month.
The details of the rape and murder revealed in the charge sheet triggered public and political outrage in various parts of the country, as many are calling for speedy justice in the case.
In connection with the case, two First Information Reports (FIRs) have been filed - one against eight people for allegedly being involved in the crime and another has been filed against a group of lawyers who allegedly stopped the police from filing the charge sheet against the eight accused.