The Denver Sheriff Department is investigating the allegations of a department captain who alleged that two deputies raped her — and that the incident led to sexual harassment and trumped-up accusations that she embezzled money from a foundation.

Capt. Cheryl Arabalo alleged the sexual assault occurred Oct. 11, 2009, and that when she reported it to a superior, he told her not to say anything about it and never reported her allegation to administrators.

But the department didn’t begin a criminal investigation of Arabalo’s allegations until this past Nov. 21 — more than two years after the incident. That investigation was launched after another department employee mentioned the alleged assault during the course of an investigation into charges that Arabalo embezzled money from the Denver Sheriffs Foundation.

“The department immediately requested a criminal investigation into the (rape allegation),” according to a statement issued by the department. “… That investigation is still ongoing, and includes (Arabalo’s) allegation that she notified her immediate supervisor the day after the incident occurred.”

The Sheriff Department operates the county jail and provides security at Denver’s courthouses.

Arabalo, 44, made the rape allegations public last month when she sought permission to add them to a sexual-harassment lawsuit she filed against the department in September. (The Denver Post normally does not name victims of sexual assault, but Arabalo agreed to be identified.) A federal magistrate judge has not yet decided whether to allow her to add to her complaint.

Arabalo alleged that Deputies William Current and Tyler Mazzotti, who were members of the foundation’s board, drugged and raped the 18-year department veteran in her home after a board meeting.

Both deputies are on investigatory leave.

“They deny any wrongdoing completely,” said their attorney, Reid Elkus.

When Arabalo reported the incident to a major, he told her that the two would claim the sex was consensual, she alleged in an interview with The Denver Post.

Arabalo didn’t separately report the incident to police.

“The culture of law enforcement is that you shut up once you have gone to your direct boss because if you don’t, what will happen to you is exactly what happened to me,” she told The Post. “They did everything they could to get rid of me.”

After she told the major about the incident, she faced sexual harassment from another officer, a captain, according to court documents.

After the department investigated the sexual-harassment charges, the captain received a 75-day suspension without pay.

“There were no disciplinary actions for almost a year — they claim they have a zero-tolerance policy, but it is really zero enforcement,” said Linda Lee, an attorney for Arabalo.

After Arabalo filed a complaint about the captain with the Colorado Division of Civil Rights, the department investigated her for filing an incorrect computer report regarding her supervision of deputies’ routine checks on inmates, according to her lawsuit.

“That was a computer issue,” Arabalo said.

Despite that, the department suspended her for 70 days after an internal investigation.

Without naming Arabalo, former Independent Monitor Richard Rosenthal said in a later report that the penalty was too light. He said she should have been demoted to deputy.

Then, last May came the allegations that Arabalo stole money from the Denver Sheriffs Foundation, which she started to provide financial assistance to active Denver sheriff officers, civilians and their families in emergency situations such as death, disability, illness, injury or other severe situations.

The investigation was launched shortly before she was scheduled to return to work from suspension.

A grand jury failed to return an indictment in the embezzlement case, Lee said.

Gutierrez, who was the foundation’s treasurer, “brought the allegation to the Denver Sheriff Department after he was accused of sexually harassing (Arabalo),” according to her lawsuit.

When Arabalo returned to work after 70 days, she was put on investigatory leave.

Her September sexual-harassment suit against the captain and the city of Denver makes no mention of the rape allegations.

Despite the lack of criminal charges in the embezzlement case, she remains on leave and is facing discipline for violating department policies that could result in her being fired, Lee said.

A department complaint charges that her conduct in the foundation case hurt the department “in some way, but the grand jury came back without an indictment,” Lee said.

“She has been on the force for 18 years without problems, then when she reports harassment she gets hammered,” Lee said. “She rose to the level of captain, but the moment she says someone sexually harassed her, she is no longer a good employee.”