Amtrak Police Chief Polly Hanson attends a news conference at Union Station in Washington, D.C. on Sept.3, 2015. She joins Homeland Security Secretary Jeh Johnson in highlighting nationwide rail safety and security efforts. (Marvin Joseph/The Washington Post)

Amtrak’s inspector general has launched a fraud and conflict of interest investigation involving the rail system’s top law enforcement officer, her “alleged boyfriend” and a counterterrorism contract she helped oversee, according to federal court documents.

Amtrak Police Chief Polly Hanson, who oversees 500 sworn officers and other personnel across the country, was deeply involved in preparing a contract that was awarded to ABS Consulting in May 2014, according to a statement from the inspector general filed in U.S. District Court for the District of Columbia.

Hanson — who also has served as chief of Metro Transit Police and executive director of the Strategic Services Bureau of the D.C. police force — failed to disclose the nature of her relationship with Kerry Thomas, senior director for Homeland Security Support Programs for ABS, the documents allege.

A statement from a senior special agent with the inspector general’s office said an investigation was initiated in December 2015, based on allegations about Hanson and Thomas’s relationship. The allegations included that Hanson and Thomas have been romantically involved for a “substantial period of time, that they cohabitate in Arlington, Va., and own a residence together in Delaware, and that, consequently, their actions regarding the procurement of the contract . . . were unethical and illegal.”

According to the court records, Hanson and Thomas are listed as having separate apartments in the same building in Arlington, Va. They are listed as co-owners of a condominium unit in Dewey Beach, Del., and share a mortgage on it.

The court documents were filed as part of a response to a civil action by Hanson to limit investigators’ access to her bank records and other financial information.

Sara E. Kropf, Hanson’s attorney, said Wednesday night that Hanson was aware of the allegations by the inspector general’s office and has cooperated fully with the investigation. She said that Hanson did disclose her personal relationship with one of the bidders and that Hanson “did not personally benefit from the award of the project at all.”

“Ms. Hanson has been a respected law enforcement officer for 40 years, has a stellar reputation and is anxious to see this matter concluded,” Kropf said.

Thomas and ABS Consulting did not respond to requests for comment.

ABS received a $713,609 contract, funded by the Department of Homeland Security, to “provide counter-terrorism, law enforcement and rail specific training courses” for Amtrak police under an initiative known as RailSafe, according to the filings. The training would “provide information and familiarity with the railroad environment” to partner law enforcement agencies across the country that help with rail system operations and emergencies, according to the documents.

In October 2015, the contract was changed to include training in 10 additional cities, bringing the total contract to $1,071,597, according to the filings.

From information “gathered thus far” by investigators, the relationship between Hanson and Thomas “is quite close and personal, and includes a ‘romantic’ relationship and a joint financial relationship that appears to go as far back as 2006,” according to a filing in May by federal prosecutors representing the inspector general in the dispute over financial records sought in the investigation.”

The filing continues: “This close personal and financial relationship was not disclosed to Amtrak prior to the award of an Amtrak contract to ABS Consulting, a company in which Thomas is a Senior Director in charge of the Amtrak contract.”

The inspector general is trying to determine whether Hanson violated federal wire- and mail-fraud laws and the federally supported railroad’s conflict-of-interest rules. The investigation into Hanson was first reported Wednesday night by WTTG-TV (Channel 5) in Washington.

Hanson was named Amtrak police chief in 2012. At the time, Amtrak’s chief executive and president, Joe Boardman, praised her “strong police, security and intelligence background” and said in a statement that she was “exactly what is needed” to improve the department.

Hanson also spent 27 years at the Metro Transit Police Department, where she started out as a police officer and was eventually promoted to chief of police. Additionally, she worked for three years for D.C. police.

The inspector general is also investigating whether Thomas and his company violated the federal False Claims Act and the contract’s terms “when they failed to disclose the relationship and the nature of the relationship to Amtrak prior to the award of the contract.”

Amtrak officials declined to comment, citing the active investigation. The inspector general’s office did not respond to a request for comment.

Thomas Hopkins, the senior special agent with the inspector general, asserted in court filings that in April 2014, Hanson sent Amtrak’s chief financial officer, who had recently been given the duties of ethics officer, an email that said, “I just learned I know the bidder at ABS Consulting.”

“The email failed to disclose that she had known Thomas for 10 years and was in a personal or financial relationship with him,” Hopkins wrote.

The ethics officer replied: “Polly, as we discussed, I do not see an issue moving forward with this purchase agreement,” according to the filings.

The ethics officer said that he did not recall that conversation but that if Hanson had told him that she had a “close personal relationship” with Thomas, as she claims to have done, he would have referred the matter to Amtrak’s legal department.

A top Amtrak procurement official and vice president said that if there had been a timely and complete disclosure of what he considers a conflict of interest, ABS would have been deemed ineligible for the contract, Hopkins wrote.

Jean-Louis Magda and Jennifer Jenkins contributed to this report.