Major General Jeffrey S. Buchanan's decision to uphold the findings of Manning's 2013 court-martial will automatically send the case to the Army Court of Criminal Appeals, an Army statement said.
The soldier, formerly known as Bradley Manning, was working as an intelligence analyst in Baghdad in 2010 when she gave the pro-transparency site WikiLeaks 700,000 documents, videos, diplomatic cables and battlefield accounts.
The trove included a 2007 video of a U.S. Apache helicopter firing at suspected insurgents in Iraq, killing a dozen people, including two Reuters news staffers.
Manning pleaded guilty to 10 charges but was convicted last year on 20 counts, including espionage and theft.
She was found not guilty of the most serious charge, aiding the enemy.
Manning's request for leniency followed an application for a presidential pardon filed last September, where her defense team maintained that she had released information to the media for the public good.
Manning's sentence was the longest ever handed down for turning over secrets to the media.