Mark Morgan, who heads the FBI training division, is the first outsider to lead the Border Patrol in its 92-year history.
He inherits a force under fire for ignoring or downplaying shootings of unarmed people and other abuses by agents, and of doing too little to stem corruption by drug cartels, smugglers and other criminals.
The Border Patrol is responsible for securing the nation's borders. Driven by concerns about national security, the number of agents and other personnel has grown dramatically in the last 15 years.
Critics say that has led to a lack of accountability and an array of other problems, from excessive use of force to racial profiling.
In a statement, R.
Morgan's career has included stints as a Los Angeles Police Department officer, as a deputy sheriff in Platt County, Mo., and 20 years at the FBI.
He ran an FBI-led Hispanic gang task force in the Los Angeles field office that focused on MS-13 and 18th Street gangs. He also held senior FBI roles in Baghdad, Iraq; New Haven, Conn.; and El Paso, Texas.
Most recently, Morgan headed training at the FBI's training center in Quantico, Va., and at FBI headquarters in Washington.
FBI Director James Comey said in a statement that Morgan brought "passion for justice and public service" to his work.
Morgan also led the internal affairs office at Customs and Border Protection in 2014, a post that put him at odds with the Border Patrol's insular culture.
Officials say he helped internal affairs overhaul how abuse cases are investigated, identified weaknesses in how agents were trained to use force, and pushed to get greater authority for internal affairs officers.
Morgan's appointment immediately took flak from the Border Patrol's powerful union, however. It complained that Kerlikowske had ignored viable candidates within the force.
"How can someone who has never made an immigration arrest in his career expect to lead an agency whose primary duty is to make immigration arrests?" asked Joshua Wilson, a spokesman for the union's local chapter in San Diego.
The union had urged Kerlikowske to choose Ronald D. Vitiello, a veteran of the Border Patrol who has served as acting chief. Vitiello improved new shift rotation schedules, Wilson said.
Some advocates of tougher immigration actions also criticized the selection of an FBI veteran over an internal candidate.
"It basically is saying that the existing border agents don't know what they are doing and need an outsider to come in from a totally separate branch of law enforcement and tell them how to do their jobs — it's offensive," said Rosemary Jenks, director of government relations for NumbersUSA, a Virginia-based advocacy group that lobbies to reduce immigration levels.
By almost any measure, the Border Patrol's problems are significant.
A separate independent review of 67 uses of deadly force made public in 2014 found that some agents had deliberately stepped in front of cars to justify shooting at drivers and had fired weapons at people throwing rocks from the Mexican side of the border.
"It is not a secret that the Border Patrol has major accountability problems resulting from years of unchecked abuse," James Lyall, an American Civil Liberties Union lawyer in Tucson, said in a telephone interview.
Morgan "needs to act promptly to implement modern law enforcement best practices that the Border Patrol has resisted for far too long," Lyall said.
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