The Pentagon is overhauling its efforts to find and identify missing service members from past wars, Defense Secretary Chuck Hagel announced Monday.

The changes address the problems laid out in an investigation by ProPublica and NPR, including outdated scientific methods, overlapping bureaucracy, a risk-averse disinterment policy for the 9,400 unknowns buried around the world, and poor laboratory management that inhibited the mission.

“The time has come for a paradigm shift,” said Acting Under Secretary of Defense for Policy Michael Lumpkin, who headed up a 30-day review of the mission Hagel ordered in February.

One of the bigger changes involves the military’s failure to embrace DNA. Our investigation detailed how the Pentagon identification effort relegated DNA to only a confirmation tool, rather than using it to lead the process as is now done in other countries.

Using a DNA-led process is “absolutely something we’re going to move toward,” Lumpkin said.

The Pentagon will “break away from the way of traditionally doing business...that didn’t fully embrace progressive science,” he said.

The Pentagon spends about $100 million a year on the MIA mission, yet it solves surprisingly few cases. Last year, the military identified just 60 service members out of the about 83,000 Americans missing from World War II, Korea and Vietnam. The lackluster efforts have been subjected to intense Congressional scrutiny and media coverage, including holding fake arrival ceremonies and mismanaging overseas excavations.

In restructuring the mission, the Pentagon is eliminating the two main agencies — the Hawaii-based Joint Prisoner of War/Missing in Action Accounting Command and the Washington-based Defense Prisoner of War Missing Personnel Office — and creating a new single agency. There will be one chain of command and one budget.

“We’re streamlining everything,” Hagel said.

The reorganization “resolves issues of duplication and inefficiency” and makes the effort “more transparent and responsive” to families, he said. The changes will be implemented over the next 18 months.

Although it’s unclear at this point what positions and personnel will be eliminated besides the commanders of JPAC and DPMO, Lumpkin insisted the as-yet-unnamed agency will be a “fundamentally new organization.”

“It’s not business as usual,” he said.

The restructuring pushes aside J-PAC’s scientific director, Tom Holland, who has held the position for 19 years. As ProPublica and NPR detailed, Holland has had nearly total control of each step in the identification process. That job will now be handled by an Armed Forces Medical Examiner.

The move appears meant to address the fact that sign-offs on the lab’s decisions were little more than a rubber stamp. Putting a medical examiner at the head of the process — someone who is scientifically knowledgeable — ensures “the opportunity for rubber stamping doesn’t exist,” Lumpkin said.

Outsiders and former J-PAC officials said the changes were promising.

“I think the Armed Forces Medical Examiners are probably as well suited to do that as anyone else I could think of,” said Mark Leney, a former JPAC anthropologist who now teaches at the University of Massachusetts Medical School.

“Selecting a scientific leader with a track record of working in an interdisciplinary scientific environment, preferably someone who has managed a large group of diverse technical and scientific experts before, will be key to making this work,” Leney said.

Hagel also announced a plan to develop public-private partnerships to “leverage capabilities” of nongovernmental groups who work on recovering and identifying MIAs – we which included last month in a rundown of potential ways to fix the effort. “I think that would be a waste if we didn't do that,” Lumpkin said.

ProPublica and NPR also reported that under Holland’s leadership the lab rejected 96 percent of potential disinterments of unknown servicemembers, despite DNA advances that could help lead to their identification.

Lumpkin said that policy will be changed, though he had no specifics.

The Pentagon is also considering a national campaign to collect DNA samples from family members of the missing.

The restructuring will create one case management system for all missing persons, which should make it simpler to conduct research and keep families informed. DPMO and JPAC, long embroiled in a turf war, have often fought over records, duplicated trips to the National Archives, and done competing investigations.

“We’re now taking concrete, enforceable steps to fix what has been a management mess—but as with any effort to demand accountability, the devil will be in the details and the implementation,” Senators Claire McCaskill, D-Mo., and Kelly Ayotte, R-N.H., said in a statement. “So we’re looking forward to working with the Pentagon to ensure the families of our missing heroes receive nothing less than honesty and transparency in our efforts to recover their loved ones.”