The warrant has been issued by an Additional Chief Judicial Magistrate court on a petition filed by the Mahesh Nagar Police station on February 26, they said.
"The missing accused has to be arrested by March 25", ACP Parasmal Jain told PTI.
On February 4, the Vasundhara Raje government had suspended Mohanty over an allegation of sexual exploitation.
He was earlier summoned by the commissionerate police to appear before them for questioning but he went reportedly missing from home, and his wife sought a week's time.
But, that too expired early this month.
An Additional Chief Secretary-rank officer Mohanty was chairman of Rajasthan Civil Services Appellate Tribunal and he was charged of rape by the victim who was preparing for civil services on February 19, 2013 at his flat .
In her complaint on January 25, the victim alleged that the IAS officer, B B Mohanty, Chairman of Rajasthan Civil Services Appellate Tribunal, had raped her repeatedly last year after promising to help her clear civil services examination.
The flat at New Sanganer Road, where the alleged exploitation had taken place, was sealed by the police last month.