There they are sentenced to death in show trials "which last between one and three minutes", according to the report.
Detainees are returned to the prison, blindfolded and transferred to its "white building".
In a dark basement room, nooses are put around their necks and they are hanged in groups of between 20 and 50 people, Amnesty said.
"Throughout the process, the victims remain blindfolded," the report states. "They are only told that they have been sentenced to death minutes before the executions are carried out; they are never told when their executions will be carried out."
The bodies are disposed of in mass graves. Medical reports usually give the cause of death as heart or lung failure, according to Amnesty.
Researchers interviewed former prisoners and guards and concluded that between 5000 and 13,000 people were killed there from September 2011 to December 2015. The killings are believed to be continuing.
Amnesty alleges that the scale of the killing means the hanging programme must have been "authorised by officials at the highest levels of government".