White House and Justice Department officials say US Army Sergeant Bowe Bergdahl submitted the clemency request. If granted, it would allow Bergdahl to avert a court-martial trial scheduled for April.
He faces charges carrying a maximum penalty of life in prison.
Bergdahl walked off his post in Afghanistan in 2009 and was held captive by the Taliban and its allies for five years.
The Obama administration's decision to swap prisoners for his return in 2014 was criticised by some Republicans.
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