Lieutenant Colonel Steven Jordan, who led a military intelligence unit that conducted interrogations at the Iraq prison, is the highest ranking officer to be charged with criminal offenses in the two-year-old Abu Ghraib scandal.
An army charge sheet alleged cruelty and maltreatment, saying Jordan "did oppress Iraqi detainees, persons subject to his orders, by subjecting them to forced nudity and intimidation by military working dogs."
He faces a total of 12 counts on seven charges.
Besides cruelty and maltreatment of prisoners, they included disobeying a superior officer, dereliction of duty, making false official statements, fraud, wrongful interference with an investigation, and false swearing.
The charges together carry a maximum possible prison term of 42 years.
However, the cruelty and maltreatment charge carries a maximum sentence of only one year in prison.
"The US Army has been conducting an investigation into this matter for over two years," an army official said.
"These things take time. They have to be done in a thorough and professional manner."
The scandal exploded into public view in 2004 after US news organizations made public now-notorious photographic images showing detainees at Abu Ghraib being sexually humiliated and abused by guards.
In some images, naked detainees were seen cowering before snarling, unmuzzled dogs.
The charge sheet said Lieutenant General Ricardo Sanchez, the commander of US forces in Iraq at the time, had issued an order requiring his permission to use "certain specified interrogation and counter-resistance techniques in the interrogation of detained Iraqi prisoners under his control, to include: use of military working dogs."
Jordan knew of the order but failed to obtain Sanchez's permission to use the dogs in interrogations, and then lied about it in subsequent statements to investigators, the charge sheets allege.
Jordan was not accused of personally mistreating prisoners. But he was "derelict in the performance of those duties in that he willfully failed to train, supervise and ensure compliance by soldiers under his control" based on official interrogation policy, the charge sheet alleged.
The alleged abuse occurred between September 17 and December 24, 2003.
Major General Antonio Taguba, who conducted the first investigation into the abuse scandal, questioned Jordan in Kuwait on February 24, 2004.
Jordan falsely told Taguba that he never saw any detainees being abused and never saw nude detainees, the charge sheet said.
Jordan allegedly made a similar false official statement on April 28, 2004 to Major General George Fay, who conducted a separate probe into the role of military intelligence in the scandal.
Jordan also was charged with disobeying orders by both Taguba and Fay not to talk to other army personnel or potential witnesses about the detainee abuse investigation.
Additionally, Jordan was accused of defrauding the government by submitting inflated repair bills for two government-owned vehicles, a Nissan and a Hyundai.