An Internal Revenue Service agent has been charged with raping and choking a summer intern in his government-issued car after inviting her for drinks after work, prosecutors said.

The Boston-based agent, James Clarke, 44 — who was indicted Wednesday on charges that include aggravated rape and strangulation — attacked the 21-year-old woman after offering her a ride to a train station from a bar on July 26, Suffolk County District Attorney Daniel Conley said.

Clarke allegedly handcuffed the intern while parked inside his IRS-owned car at the Government Center garage in Boston, where he “assaulted her with his service firearm and subjected her to sexual acts against her will,” according to the district attorney’s office.

Clarke then drove the victim to South Station and allegedly assaulted her inside the car again. The woman immediately called police and was later treated at a hospital.

Clarke’s attorney, Michael Doolin, told the Boston Globe that the married father of three “adamantly denies” the allegations.

“He’s cooperated with the investigation from the moment he was notified of it, and he looks forward to taking this case to court and being vindicated,” Doolin told the newspaper, declining further comment.

Police in Boston interviewed Clarke the day after the alleged attack and investigators seized his firearm and vehicle for testing, but he wasn’t arrested, the Globe reports.

Jake Wark, a spokesman for Conley, said the decision not to immediately arrest Clarke was “not unusual” when a defendant is aware of an investigation and makes no effort to flee.

The Globe first reported on the allegations against Clarke in November, noting at the time that he was allowed to continue working for the agency despite an ongoing investigation into the July incident. Clarke’s duties appeared limited by November, however, as neither his .40-caliber Glock nor his tan, four-door sedan owned by the government had been returned to him, sources told the Globe at the time.

Clarke’s arraignment was scheduled for April 5.