Sub Inspector of Rynjah police station in the city S N Roy is absconding since April 13 after applying for sick leave.
Superintendent of Police (City) M Kharkrang today said the arrest warrant was issued against the SI based on the victims statement in the court.
The department has also suspended the officer, he said.
Kharkrang said the police have conducted raids in several places to trace Roy but he has gone hiding since his name began to appear in the crime.
His sick leave has not yet been granted by the competent authority, he added.
The 13-year-old victim, a class VIII student of a city school, was gang-raped at a city hotel last month.
The police so far have arrested four persons in this connection - Bobby Jyrwa Nongseij, Johny Kshiar, Brando Nongrum and one girl who abetted the crime, Angel Dulian.