Matthew Klein, the head of internal affairs for Customs and Border Protection. Credit: Courtesy of U.S. Customs and Border Protection

The head of internal affairs for U.S. Customs and Border Protection, the nation’s largest law enforcement agency, has resigned, according to an email obtained by Reveal from The Center for Investigative Reporting.

Matthew Klein is the latest top official to leave the agency’s internal watchdog office, which has been run by at least three people since Commissioner R. Gil Kerlikowske took over the agency in March 2014. The reason for his departure was not immediately clear.

“As Assistant Commissioner, Mr. Klein played a critical role reinforcing CBP’s commitment to integrity and promoting accountability and transparency,” Kerlikowske wrote in a Dec. 13 email to the agency.

Kerlikowske credited Klein with leading efforts to investigate use-of-force incidents. During his tenure the agency solidified a national review board that examined shootings and other violent confrontations, sped up investigations, built coalitions with other internal watchdogs that had battled with the agency in the past and worked with an advisory panel to improve integrity and mitigate corruption, Kerlikowske wrote.

Matthew Klein, the head of internal affairs for Customs and Border Protection, recently resigned from his post, according to an email sent to employees of the nation’s largest law enforcement agency. Credit: Courtesy of  U.S. Customs and Border Protection

Klein, who joined Customs and Border Protection as the assistant commissioner for its office of professional responsibility in June 2015, did not return calls for comment. An agency spokesman did not return emails asking for comment.

Since Kerlikowske took over the agency in 2014, Customs and Border Protection has pushed for greater transparency and accountability. Under his leadership, the internal affairs office gained the authority to investigate crimes and not just administrative violations. Yet the agency, which is part of the U.S. Department of Homeland Security, has come under fire from former officials and civil rights groups for its use of deadly force and the fact that all shootings and other violent incidents examined by the review board have been deemed justified. Two former top internal affairs officials recently railed against the Border Patrol’s militarized approach to security and its culture of coverup in a U.S. Supreme Court amicus brief filed Dec. 9.

Since 2010, more than four dozen people have been killed during confrontations with Customs and Border Protection agents and officers. In that time, one agent has faced federal charges for homicide, with a trial slated to begin in February. More than 170 employees have been charged with or arrested on suspicion of corruption-related crimes since 2004, including the Dec. 14 arrest of a Border Patrol agent near San Diego by an FBI-led anti-corruption task force.

The internal affairs office, which is now known as the Office of Professional Responsibility, has been roiled by turnover, infighting and turf battles with other watchdog agencies, including the Department of Homeland Security’s Office of Inspector General. A panel of experts who sit on the Homeland Security Advisory Council, which advises Secretary Jeh Johnson, has said the office is woefully understaffed to police corruption, the use of force and other personnel matters.

James F. Tomsheck, who ran the internal affairs office from June 2006 until his ouster in June 2014, has become a vocal critic of Customs and Border Protection since his departure. Tomsheck was temporarily replaced by an FBI agent, Mark Morgan, who returned to Customs and Border Protection last summer as chief of the U.S. Border Patrol.

Klein previously held several high-ranking positions with the Washington, D.C., Metropolitan Police Department, including commander of internal affairs and recruiting and background investigations divisions and director of civil rights and force investigations.

Andrew Becker is a reporter for Reveal, covering border, national and homeland security issues, as well as weapons and gun trafficking. He has focused on waste, fraud and abuse – with stories ranging from border corruption to the expanding use of drones and unmanned aerial vehicles, from the militarization of police to the intersection of politics and policy related to immigration, from terrorism to drug trafficking. Becker's reporting has appeared in The Washington Post, the Los Angeles Times, The New York Times, Newsweek/The Daily Beast and on National Public Radio and PBS/FRONTLINE, among others. He received a master's degree in journalism from UC Berkeley. Becker is based in Reveal's Emeryville, California, office.