In a statement released on Monday, the watchdog added that all detainees in Iraq should be released – given the hand over of authority to Baghdad.
"The USA has announced that it intends to continue to hold, without charge, between 4000 and 5000 detainees without clarifying on what legal basis it will do so," the group said.
"Yet if, as the UN resolution  proclaims, occupation effectively ends with the handover, then international humanitarian law requires that all prisoners of war, detainees and internees must be released by the occupying powers."
Amnesty said it had received no reply to a 9 June letter it wrote to the US envoy to the United Nations, John Negroponte - the US ambassador to Iraq.
The letter expressed serious concern that UN resolution 1546 fails to clarify what would happen to the thousands of prisoners held by the occupying powers.
"Any further detentions by the US and other members of the multinational force after the handover would be unlawful," the rights group said.
"If ... occupation effectively ends with the handover, then international humanitarian law requires that all prisoners of war ... be released"
"They may only be re-arrested by the Iraqi authorities if there are grounds under Iraqi law, consistent with international standards, to detain them."
Need for accountability
The statement coincided with the publication of a report Iraq: Human Rights Protection and Promotion Vital in the Transitional Period.
In the new document, Amnesty urged all foreign troops and contracted militias on the ground in Iraq to abide by international law.
"It is vital that clear lines of accountability and responsibility be established for all those who continue in detention," the rights group said.