Retired Maj. Gen. Kelly McKeague, a 1977 Damien Memorial School graduate, was named director of the Defense POW/MIA Accounting Agency on Tuesday, returning to the program that was mired in controversy several years ago.

The agency that searches for, recovers and identifies missing American war dead has not had a permanent director since Michael Linnington left in June 2016.

DPAA, which replaced the former Joint POW/MIA Accounting Command, has an $85 million lab and offices at Joint Base Pearl Harbor-­­Hickam. More than 400 personnel are based in Hawaii.

McKeague, who was born in Liliha and grew up in Papakolea, was sworn in during a morning ceremony at the Pentagon. He’ll be working out of DPAA’s office in Washington, officials said.

“I know the importance of the agency’s mission and I look forward to working with DPAA’s team of dedicated professionals,” McKeague said in a news release.

Fern Sumpter Winbush, who was serving as acting director, will resume her role as principal deputy director for the agency, responsible for formulating policy, overseeing business development and increasing outreach initiatives, the Pentagon said.

McKeague, who has served as an independent business consultant since his retirement from the Air Force in 2016, is no stranger to DPAA and its forerunner, JPAC.

McKeague was the last commander of JPAC before it was renamed DPAA in an organizational shake-up in early 2015. The Defense POW/Missing Personnel Office, JPAC and some functions of the Air Force’s Life Sciences Equipment Laboratory merged to create DPAA.

McKeague took command of JPAC in late 2012, inheriting an MIA recovery mission plagued by inefficiency. That effort, conducted by a handful of agencies around the country, was fragmented, redundant and hampered by interagency disputes, a July 2013 Government Accountability Office report said.

The Defense Department reform followed a series of embarrassing revelations in reports and congressional testimony starting in 2013. Paul M. Cole, who was on a scientific fellowship at JPAC, said in an internal efficiency report that past missions to Europe “did not appear to be rigorous, demanding, or an imposition on anyone who enjoys luxury accommodations, fine hotels and top-tier cuisine.”

A 2010 mission to Italy saw four JPAC team members stay five nights at the Grand Hotel de la Minerva, where room rates started at $500 a night, Cole said at the time.

In March 2014 then-Defense Secretary Chuck Hagel announced he was overhauling and combining JPAC and the other Pentagon accounting units. McKeague was tapped for the post of deputy director based in Hawaii. He left the agency in September 2015 with the arrival of Army Brig. Gen. Mark Spindler as the new deputy director.

Linnington, a retired Army lieutenant general, was named DPAA’s first permanent director in June 2015. He resigned a year later to become chief executive officer of the Wounded Warrior Project.

Congress mandated in 2009 that the Pentagon have the capacity to identify 200 MIAs a year by fiscal 2015 — a goal the agency has struggled with ever since as it has gone through the reorganization.

The agency, which has a budget of $112 million, said it has made 172 identifications so far this fiscal year, which ends Sept. 30. Last year it made 164 IDs.

Amid mounting pressure from Congress to make more IDs, the Pentagon took the unprecedented step of ordering the disinterment of all of the USS Oklahoma’s 388 casualties buried as “unknowns” at Punchbowl cemetery in order to identify the crew members from the Pearl Harbor attack.