WASHINGTON » The head of the Pentagon’s new agency in charge of recovering and identifying remains of U.S. war dead said he will push for more cooperation with private groups that have resources and interest to help reinvigorate a troubled POW-MIA accounting mission.

Michael Linnington, a recently retired three-star Army general and veteran of combat in Iraq and Afghanistan, took over the Defense POW-MIA Accounting Agency in late June and intends to complete its reorganization by the end of the year. His agency was created by merging the two offices previously in charge.

He has little experience in the MIA mission but said last week that he knows its history is riddled with controversy as well as criticism from Congress and groups that advocate for families of the missing.

“I am aware of some of the reports on the dysfunction,” he said, referring to 2013 reports of deep conflict among multiple agencies previously assigned to the accounting mission. “Whenever you have disparate organizations all focused in the same area, there’s going to be a natural tendency to step on each other.”

Linnington said he sees promise in working more extensively with private groups like History Flight, a Florida-based group that has worked with the Pentagon in recovering war remains abroad, including dozens of Marines killed in the World War II battle of Tarawa in the Pacific.

The POW-MIA agency has faced heavy criticism from veterans and MIA family advocacy groups. “I don’t mind criticism,” Linnington said. “I applaud criticism.”

The POW-MIA accounting effort, while far more aggressive and extensive than similar undertakings by any other country, has suffered from many problems over many decades. Last July, the AP disclosed an internal Pentagon report that said the organization responsible for finding and recovering remains on foreign battlefields and identifying them at a Hawaii-based government laboratory was wasteful, acutely dysfunctional and often mismanaged.

Shortly after the AP report, the Government Accountability Office issued a report saying the MIA accounting effort was hampered by weak leadership, infighting and a fragmented approach to planning. The report recommended a more streamlined chain of command and other organizational changes, which are now being implemented.

Together the reports prompted calls in Congress to ensure that the government lives up to its pledge to account for as many MIAs as possible. Congress in 2009 set a legal requirement that the Pentagon identify at least 200 remains a year by 2015. It has not come close to that figure in recent years and almost certainly will not reach it this year, with only 34 accounted for so far, according to figures provided by the Pentagon.