An FBI veteran was named Monday to head the U.S. Border Patrol, a departure from the historical practice of picking someone who has risen through the ranks.

Mark Morgan, who briefly led the internal affairs department at the Border Patrol's parent agency, will oversee a multibillion-dollar annual budget as he runs the agency in the crosshairs of the national debate about border security and immigration.

His selection didn't reflect lack of confidence in the Border Patrol's leadership or performance, Customs and Border Protection Commissioner R. Gil Kerlikowske emphasized.

Almost all federal law enforcement agencies — from the Coast Guard to the Drug Enforcement Administration — had outsiders take over at one time, Kerlikowske said.

"In the case of the Border Patrol, the current leadership across the top, from headquarters to the field, consists of the finest group of men and women that I have worked with in my more than 40 years in law enforcement," he wrote in a memo to staff.

Morgan is no stranger to the Border Patrol. In 2014, the FBI loaned Morgan to Customs and Border Protection to serve as acting assistant commissioner for internal affairs. He oversaw an extensive review of complaints of excessive use of force and employee misconduct.

Morgan is currently an assistant FBI chief who leads the training division. He joined the FBI as an agent in Los Angeles in 1996 and has held various positions, including head of its El Paso, Texas, office.

"Mark's outstanding investigative work and leadership have been an incredible asset to the FBI, and he will be missed," FBI Director James Comey said.

Morgan replaces Michael Fisher, who retired in 2015 after five years on the job. Ronald Vitiello, who was deputy chief under Fisher, has been serving as interim chief. Morgan's appointment is not subject to congressional approval.

The appointment may be one of the last significant acts by Kerlikowske as commissioner of the nation's largest law enforcement agency. Commissioners are typically replaced when presidential administrations change.

The former Seattle police chief said he considered applicants from within and outside the Border Patrol.