The US military still wants to run a section of the jail and is not handing over some detainees, saying it has the right to hold insurgents caught on the battlefield, the report said.
The US is concerned that some top-level inmates could be released or tortured if they are handed over.
The Bagram prison has been described as 'Afghanistan's Guantanamo' for prisoner abuse and indefinite detention.
In April 2010, a BBC investigation uncovered allegations of prisoner abuse at a hidden facility at Bagram.
The US military, however, denied it was operating a secret jail.
In January 2012, Afghan investigators accused the US army of abusing detainees at the Bagram prison.
According to the report, the investigators said prisoners had reported being tortured, held without evidence and subjected to humiliating body searches.