Indictments charge Clarke with aggravated rape, rape, strangulation, indecent assault and battery, and assault and battery with a dangerous weapon. He was not arrested but was ordered to appear in Suffolk Superior Court for arraignment on April 5.

James R. Clarke, an agent in the IRS’s criminal investigations office in Boston, allegedly handcuffed and assaulted the 21-year-old college student at gunpoint in July, according to the Suffolk County district attorney’s office.

An Internal Revenue Service agent, who was allowed to remain on the job for months despite allegations of sexually assaulting a summer intern, was charged Wednesday with raping and choking the woman in his government-issued car.


Clarke has continued to work for the federal agency since the woman called 911 and accused him of placing a gun in her mouth and assaulting her, according to a person with knowledge of his work status.

The IRS declined to comment Wednesday on whether Clarke has been placed on leave since the indictments.

The Globe first reported on the alleged assault in November, noting that Clarke had not been arrested and was allowed to continue working at the IRS despite the ongoing investigation.

The young woman, who was not identified in documents, worked for the IRS as an unpaid intern and investigative analyst, assisting agents working on criminal investigations.

Clarke, who turns 44 on Thursday, allegedly invited her for drinks after work on July 26. They met at the Kinsale, an Irish pub at Center Plaza, across the street from the IRS offices in the John F. Kennedy Federal Building, several people familiar with the investigation told the Globe in November.

The indictments allege that Clarke offered the woman a ride to the train station, then handcuffed her while parked in his IRS-owned car in the Government Center Garage in Boston. He allegedly assaulted her with his government-issued handgun and “subjected her to sexual acts against her will,” according to the DA’s office.


The agent drove her to South Station and allegedly assaulted her again inside the car, according to authorities.

“She called police immediately afterward and was treated at a hospital,” according to District Attorney Daniel Conley’s office.

Attorney Michael Doolin, who represents Clarke, said the agent “adamantly denies these 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 said.

He declined to comment further on the case.

The woman called 911 minutes after getting out of the car and reported that Clarke had sexually assaulted her at gunpoint, according to audio transmissions recorded by Broadcastify.

Audio to go with Sunday’s IRS story. Share Email to a Friend Embed Audio to go with Sunday's IRS story.

“Caller is a female, says he put a gun in her mouth and sexually assaulted her,” the 911 dispatcher announced over the Boston police radio system just after 10:30 p.m., directing officers to South Station.

“We’ve got the victim,” an officer radioed back after locating the woman at the train terminal, according to the audio of the transmissions. “I got the suspect’s name. It’s Jamie Clarke . . . he’s an investigator with the IRS.”

Boston police said Clarke was interviewed the next day, and police seized his firearm and car for testing. He was never arrested.

After announcing the charges against Clarke on Wednesday, Jake Wark, a spokesman for Conley, said, “The joint investigation by Boston police and Suffolk prosecutors entailed multiple interviews, forensic testing, a review of medical records, and an exhaustive grand jury presentation to build the strongest case possible.”


He said the decision not to arrest Clarke, but to rely on him to show up in court, was not uncommon.

“It’s not unusual for a defendant to be summonsed in for arraignment when he or she is aware of the investigation and the likelihood of charges and makes no move to flee those charges,” Wark said.

Clarke, a lawyer who is married with three children, investigated financial crimes, including money laundering, identity theft, and tax evasion. He was assigned last summer to a Drug Enforcement Administration task force. The DEA dropped him from the task force in November after inquiries from the Globe.

Shelley Murphy can be reached at shelley.murphy@globe.com. Follow her on Twitter @shelleymurph.