A former Army three-star general has taken over leadership of the Pentagon mission of investigating, recovering and identifying missing American war dead following a shakeup in the effort spread among agencies in Hawaii, Nebraska, Ohio and Washington, D.C.

Lt. Gen. Michael Linnington retired prior to taking the civilian senior executive service position as the new director of the Defense POW/MIA Accounting Agency, said Air Force Lt. Col. Melinda Morgan, a DPAA spokeswoman.

A 1980 West Point graduate, Linnington was military deputy to the undersecretary of defense for personnel and readiness. In January he was named an adviser to the MIA effort.

Linnington started in the new role Monday. He will work out of Arlington, Va., near the Pentagon, pending any decision to move the headquarters, Morgan said.

He took over command of the DPAA from Navy Vice Adm. Mike Franken, who was named interim director of the agency in January.

The DPAA is an amalgamation of the former Joint POW/MIA Accounting Command, based in Hawaii; the Defense POW/Missing Personnel Office in Washington, D.C.; and some functions of the Air Force’s Life Sciences Equipment Laboratory in Ohio.

The former JPAC, located at Joint Base Pearl Harbor-Hickam, also has a satellite lab in Nebraska.

Until January, JPAC was commanded by Air Force Maj. Gen. Kelly McKeague, who was born in Liliha, grew up in Papakolea and graduated in 1977 from Damien Memorial School. McKeague more recently served as interim deputy director of the Pentagon MIA effort.

McKeague, “who has served this mission admirably for nearly three years, will be rotating (out) this summer,” Morgan said.

The military services have provided nominations for the deputy director job, and a selection will be announced in coming weeks, she said.

“As the (Defense Department) works to reorganize its efforts to account for missing personnel into a single, accountable and responsive organization it has been key to establish comprehensive oversight of the personnel accounting resources, research and operations,” Morgan said in an email. “Vice Adm. Franken began this process knowing it would be carried on by civilian leadership and we look forward to Director Linnington’s leadership as DPAA continues on this significant path of reorganization.”

The Pentagon’s efforts at reform followed a series of embarrassing revelations in reports and testimony before Congress starting in 2013 concerning failures in the effort to identify missing American war dead.

The MIA effort, conducted by a handful of agencies around the country, was fragmented, complicated by overlapping functions and interagency disputes.

Then-Defense Secretary Chuck Hagel said last year that Congress had mandated that the Pentagon have the capacity to identify up to 200 sets of remains a year as of 2015, but that in 2013 the agencies identified only 70 sets.

At the time, Hagel directed the Defense Department to reorganize its efforts into a single, accountable organization with comprehensive oversight of MIA operations.

A new $85 million lab — the Sen. Daniel K. Inouye Defense POW/MIA Accounting Agency building — provides 140,000 square feet of laboratory, administrative and storage space at Hickam.

The Pentagon announced in April that it would take the unprecedented step of exhuming the remains of up to 388 sailors and Marines who were on the USS Oklahoma and killed on Dec. 7, 1941, at Pearl Harbor and buried as “unknowns” at Punchbowl.

Upon disinterment, which has started, the Oklahoma remains will be transferred to the Hickam lab for identification and eventual return to families. The step is seen as one way to increase the number of annual MIA identifications.