Lieutenant Colonel Steven Jordan was charged by the military district of Washington on Friday.
He faces 12 criminal counts relating to seven different charges, making him the highest-ranking person charged in the prison abuse scandal.
Ten low-ranking soldiers have been convicted in military courts in connection with the physical abuse and sexual humiliation of detainees at Abu Ghraib.
Two officers senior to Jordan at Abu Ghraib have been disciplined by the army, but neither faced criminal charges.
The charges against Jordan include cruelty and maltreatment of detainees, dereliction of duty, wrongful interference with an investigation, making false official statements and other counts.
Images of the abuse first became public on April 28, 2004, two years ago to the day before the charges were brought against Jordan.
Jordan was in charge of the military's Joint Interrogation and Debriefing Centre at the prison in the autumn and winter of 2003 at the height of the detainee abuse by US forces.
"It's gratifying that the military is beginning to focus on the role of more senior officers in the torture scandal. But this is but a step. The problems are just so clearly systemic that they need to be looked at more comprehensively"
Hina Shamsi, lawyer,
Human Rights First
Hina Shamsi, a lawyer with the rights group Human Rights First, called for more comprehensive treatment of such violations.
"It's gratifying that the military is beginning to focus on the role of more senior officers in the torture scandal," Shamsi said.
"But this is but a step. The problems are just so clearly systemic that they need to be looked at more comprehensively."