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WASHINGTON — Defense Secretary Chuck Hagel apologized Wednesday to former Army Capt. William Swenson for the mishandling of his Medal of Honor nomination four years after his heroism in a deadly six-hour battle in Afghanistan.

“We’re sorry that you and your family had to endure through that, but you did and you handled it right,” Hagel said.

Swenson, of Seattle, received the military’s top honor from President Obama at the White House on Tuesday, two years after Obama bestowed the Medal of Honor on another participant in the Sept. 8, 2009, Battle of Ganjgal Valley, Marine Sgt. Dakota Meyer.

A McClatchy investigation determined that crucial portions of Meyer’s accounts of his role in the battle were either untrue, unsubstantiated or exaggerated. The probe challenged accounts by the Marine Corps and the White House of how Meyer helped extract casualties under fire.

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The investigation also revealed that Swenson’s Medal of Honor nomination from December 2009 had inexplicably vanished from every military computer system midway through the approval process.

By contrast, Meyer’s nomination sped through the approval process and led to a book contract, high-profile media appearances and celebrity that he has used to help jobless veterans find work.

Hagel said Swenson displayed uncommon courage on the battlefield in 2009 and in his subsequent willingness to challenge senior commanders.

“He questioned — he dared to question — the institution he was faithful to and loyal to,” Hagel said at a ceremony Wednesday in which Swenson was inducted into the Pentagon’s Hall of Heroes. “Mistakes were made in his case.”

Army Secretary John McHugh, appearing with Hagel, announced major reforms in how the Army handles Medal of Honor nominations. He directed that all nominations for the award be sent immediately to Army headquarters as soon as the package is created at the battalion level.

Five Americans and 10 Afghans died in the Battle of Ganjgal against about 60 Taliban-led insurgents. Two Army officers later received career-ending reprimands for dereliction of duty by ignoring calls from Swenson and others for air and artillery support for 90 minutes as the fighting raged.

Five days after the battle, Swenson told military investigators that the delay in sending reinforcements was tied to politically driven rules-of-engagement concerns over civilian casualties.

“Now, that’s courage and that’s character,” Hagel said of Swenson’s willingness to question the rules of engagement. “As the institution itself reflected on that same courage and integrity institutionally, the institution, the United States Army, corrected the mistake. They went back and acknowledged a mistake was made, and they fixed it.”

Swenson, 34, resigned from the Army in February 2011. He is unemployed.

His request to return to the Army is expected to be approved.

Outside the White House on Tuesday, after Obama had draped the Medal of Honor around his neck, Swenson said it did not belong to him alone.

“Today I stand with the Medal of Honor,” he said. “But this award is earned with a team, a team of our finest. Marines, Army, Air Force, Navy and our Afghan partners standing side by side. And now that team includes Gold Star families who lost their fathers, sons and husbands that day. This medal represents them. It represents us.”

Swenson is the 13th Medal of Honor recipient from the Afghanistan and Iraq wars. He’s the first living Army officer nominated for the award in four decades.

“The Battle of Ganjgal was ferocious, and it was tragic, and we lost so many good lives that day,” McHugh said Wednesday. “But following the violence and the death came inspiration. We are inspired by those who fought there, by those who would not accept defeat.”

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