Updated

A Boston-based IRS agent was indicted on Wednesday on multiple charges, including rape and assault of a former intern. He was reportedly allowed to keep his job despite the explosive allegations.

James Clarke, 44, was charged with aggravated rape, rape, indecent assault and battery, strangulation and assault and battery with a dangerous weapon. He is accused of assaulting a 21-year-old woman after inviting her out for drinks, the Suffolk County district attorney said.

Clarke invited the college student out for drinks after work on July 26, 2017, and offered to drive her to South Station to catch a train.

That’s when, according to district attorney's office, he handcuffed the woman “while parked in his IRS-owned vehicle” in a parking garage, assaulted her with his service firearm and then forced her to engage in sexual acts “against her will.”

The woman, who has not been named by the authorities, called police after Clarke left her at South Station, and she was later transported to the hospital.

According to The Boston Globe, which first reported the story in November, Clarke remained with the IRS despite an ongoing investigation. The Globe reported on Wednesday that IRS did not comment on whether he'd been placed on leave since the charges were brought.

A joint investigation by the Boston Police Department’s Sexual Assault Unit and the Suffolk’s DA led to Clarke’s indictment.

He was not arrested but according to the DA’s office it is “procedural practice” that has nothing to do with his employment status at the IRS.

Clarke’s attorney, Michael Doolin, said Wednesday his client denies the allegations and “looks forward to being vindicated” in court.

Clarke is to be arraigned on April 5.

The Associated Press contributed to this report.