According to reports, the woman has alleged in her complaint that Mohanty, had called her to a place in Swej farm and raped her repeatedly on February 17 and 19 last year.
On Saturday, an FIR was registered against Mohanty.
"We have received a complaint from a local court in which the woman, aged around 23 years, had alleged that IAS officer B B Mohanty had raped her on different locations in February last year," Mahesh Nagar police station SHO Ramavtar Singh said.
He refused to divulge further details, saying he was in touch with his higher-ups with regard of the complaint.
Mohanty has rejected the allegations as "baseless" and "nonsense".
Police sources said the complainant had alleged that Mohanty sexually exploited and raped her promising to help her in IAS exam preparations.
"The court ordered police to lodge a first information report (FIR). The report was lodged on Saturday," Inspector said.
The officer said that as per the girl, her hostel is near the Indian Administrative Service's (IAS) officer flat.
"She says that Mohanty introduced himself as a senior IAS officer last year and started exploiting her on the promise of helping her clear the IAS examination. She says that the officer sexually exploiting her for the first time on Feb 19 last year at his flat," said the officer.
An investigation has been launched into the allegations, he said.
When contacted, 58-year-old Mohanty, who is the Chairman of Rajasthan Civil Services Appellate Tribunal, said he was not aware of any complaint.
He rejected the allegations as "baseless". "This is all nonsense... the allegations against me are baseless," Mohanty said.
(With Agency inputs)