A New Jersey state trooper alleges that she was sexually assaulted by a commanding officer, sexually harassed in the academy by a female commander, and repeatedly abused at the hands of colleagues.

In a federal lawsuit filed late Tuesday, Trooper Alexis Hayes makes sweeping allegations against six individuals and the state police administration, saying it conducted an internal investigation to humiliate her while never taking appropriate action in the case.

"The state police have turned Hayes - the victim - into an object of disdain and have subjected her to repeated hostile interrogations while implying that Hayes somehow bore ill will against her tormentors," the lawsuit says. "In consequence, Hayes suffered deep emotional trauma."

Hayes, 29, of Berlin, seeks monetary damages, dismissal of the accused abusers, and changes in the agency. Her lawsuit alleges that the agency, with 3,035 members, hazed those in training, ignored sexual misconduct, and closed ranks when she sought help.

Davy Jones, president of the State Troopers Fraternal Association, called the allegations "troubling" and said he intended to make sure they were "fully vetted."

"The allegations are of grave concern to me, from the onset of her career until now, and the victimizations that took place demand a complete and thorough investigation," Jones said.

State officials said yesterday that they were aware of the allegations but could not comment on pending litigation.

"The New Jersey State Police treats any allegation of misconduct very seriously. As with all allegations of misconduct, these allegations will be vigorously and thoroughly investigated," State Police Capt. Gerald Lewis Jr. said in a statement released late yesterday.

Lee Moore, spokesman for the state Attorney General's Office, said that as a matter of practice, officials do not comment on pending litigation.

The lawsuit alleges that the Attorney General's Office had been aware of the initial allegations since 2006, when an anonymous complaint was filed with the state Equal Opportunity Office.

According to the lawsuit, filed by Moorestown lawyer William Buckman, Hayes had been subjected to abusive and demeaning practices since entering the academy in 2005.

That year, an academy instructor, Sgt. Christine Shallcross, who called Hayes "Peanut," repeatedly demeaned her, the suit alleges. Shallcross once grabbed Hayes' necktie with such force that the clasp broke, according to the suit. At another time, Hayes was ordered to stand at attention while Shallcross drew on her face with a black permanent marker, the suit said.

Hayes "was required to remain standing at attention while Shallcross then chased another female trooper around and stabbed that other trooper in the neck with the marker, leaving a bruise," the lawsuit said.

After her graduation celebration, Hayes alleges, Shallcross tried to give her phone number, whispered in her ear, "Hayes, I love you," and kissed her on the cheek as Hayes was trying to leave with her sister.

Shallcross, now working on internal-affairs investigations for the state police, said yesterday she was familiar with the allegations but could not comment on them.

The lawsuit alleges that during an internal investigation, Hayes was subjected to "lengthy questioning" numerous times and that officials tried to convince Hayes that Shallcross' treatment was nothing more than mere "camaraderie."

When Hayes was assigned to the same tactical unit in South Jersey as Lt. Thomas King, the lawsuit says, King began sending her text messages at all hours and showed up unannounced at her house once this year.

Hayes alleges that King, an acting captain, sexually assaulted her in April, when she was assigned to a detail of 49 officers sent to participate in the funeral of three officers slain in Pittsburgh.

During a night of drinking, she alleges, King "continually" made sure that she had a full drink, and she returned to her hotel room "woozy from so much alcohol," the lawsuit said.

The lawsuit says that King "somehow obtained" a copy of Hayes' room key and that while Hayes was in bed, "inebriated," King sexually assaulted her. The lawsuit says she became pregnant as a result and later terminated the pregnancy.

King could not be reached for comment.

On numerous other occasions, Hayes alleges, King made sexual advances. In June, the lawsuit alleges, King assaulted her with pepper spray in front of others who did nothing to stop him, the lawsuit said.

Buckman, Hayes' attorney, said Hayes reported the alleged assault to authorities in the Pittsburgh area and tried to get a job transfer. It was unclear yesterday when the alleged assault was reported or how it was handled.

Buckman said that rather than help Hayes, state police authorities used their internal investigation as "a mechanism" to stop the complaints about superiors and other troopers.

"Their real job is to whitewash things," he said.

Buckman is recognized nationally for his role in exposing racial profiling on the New Jersey Turnpike, where minorities were disproportionately targeted for traffic stops and searches. He also went after the Lords of Discipline, a reputed secret society of state troopers who allegedly hazed others in their ranks. Though the state denied the group existed, it disciplined seven officers and settled harassment lawsuits that exceeded $1 million.

In her lawsuit, Hayes says she went to see the director of the State Police Employee Assistance Program, a confidential counseling service. The lawsuit said she then received a call from a lieutenant colonel who told her she "had to bear up with the imperfect conditions of the New Jersey State Police and go about her duties."

Eventually, Hayes went out on sick leave after suffering a "nervous breakdown," the lawsuit said.

The lawsuit also said that when Hayes was involved in a car accident in October, state police officials met her at the hospital and "refused to let [Hayes] obtain treatment until they forcibly extracted blood from her in an apparent effort to charge [Hayes] with intoxicated driving."

The lawsuit asks for an independent monitor of the state police "in light of the outrageous and corrupt method by which the New Jersey State Police abuses its powers against its members, and then uses its internal-affairs mechanisms to cover up those abuses."