President Barack Obama honored a former US Army captain on Tuesday after a long dispute that saw the soldier's nomination for the Medal of Honor stalled for years.

Captain William Swenson, 34, received America's highest military decoration at an emotional White House ceremony that follows a protracted argument over what happened in a ferocious battle four years ago in eastern Afghanistan.

Swenson, clad in a dark blue dress uniform, fought back tears as Obama paid tribute to fallen comrades who the officer tried to save after an ambush on September 8, 2009.

The Medal of Honor citation praises Swenson's "extraordinary heroism above and beyond the call of duty" for risking his life repeatedly to rescue wounded soldiers and retrieve American troops killed on the battlefield.

Obama portrayed Swenson as a man of compassion, describing a recently released video from helicopter pilots that shows the Army captain helping a seriously wounded soldier onto a chopper.

"And then amidst the whipping wind and the deafening roar of the helicopter blades, he does something unexpected," Obama said.

"He leans in and kisses the wounded soldier on the head. A simple act of compassion and loyalty to a brother in arms."

Swenson is only the sixth living recipient to be given the Medal of Honor for the wars in Iraq or Afghanistan.

He was nominated for the Medal of Honor in December 2009, but Army officials said his paperwork was "lost."

His nomination was resubmitted in July 2011 by the then commander in Afghanistan, General John Allen.

Swenson's supporters allege commanders tried to discredit him and deny him the medal because he complained to military investigators that repeated requests for air strikes and artillery fire went unheeded.

The circumstances of the delayed decoration are now the subject of a Pentagon investigation.

Another soldier in the same battle, Corporal Dakota Meyer, received the Medal of Honor in September 2011. Swenson's description of events differs from Meyer's, and the two soldiers' lives have taken different paths.

Meyer has won fame with a book, while Swenson has been unemployed since leaving the military in 2011 after what he has called his "forced early retirement."

Tuesday's ceremony served as a partial vindication for Swenson, who has kept a low-profile in the years since one of the 12-year-old war's most notorious firefights.

"I have to say Will is a pretty low-key guy," Obama said. "His idea of a good time isn't a big ceremony like this one. He'd rather be somewhere up in the mountains or on a trail surrounded by cedar trees instead of cameras."

An official military account of the battle says "Swenson braved intense enemy fire, and willfully put his life in danger against the enemy's main effort, multiple times, in service of his fallen and wounded comrades, his unit, his country, and his endangered Afghan partners."

The harrowing six-hour clash in Kunar province saw 50 to 60 insurgents ambush Afghan troops and US military trainers at dawn as they arrived for planned meetings with local elders in the village of Ganjgal.

The Americans and Afghans faced a barrage of rocket-propelled grenades, mortar bombs and machinegun fire from insurgents who had been lying in wait in the hills of the rugged Ganjgal valley.

Five American and nine Afghan troops, as well as an Afghan translator, were killed. Two dozen Afghans and four Americans, including Swenson, were wounded.

A reporter with McClatchy Newspapers who accompanied the troops in the battle, Jonathan Landay, witnessed Swenson calling for air and artillery support on the radio as Taliban insurgents had the Americans pinned down behind a stone wall.

The artillery fire request was rejected by superiors who were following new rules designed to avoid civilian casualties, and US attack helicopters did not arrive for more than an hour.

A subsequent military investigation resulted in disciplinary action against two officers over their response to the attack.

The ceremony comes as the United States wraps up the war in Afghanistan, where the bulk of US combat forces are due to withdraw next year. But Obama reminded the audience there were still 51,000 American boots on the ground.