The report contains allegations from former detainees who claim they were beaten with plastic cables, given electric shocks and made to stand in a flooded room as an electrical current was passed through the water.
Amnesty said researchers conducted interviews last year in Jordan and Iraq with former detainees, relatives of current detainees and lawyers involved in detainees' cases in Iraq.
Responding to the report a US military detention mission spokesman said that all detainees are treated according to international conventions and Iraqi law.
"Some of the detainees have been held for over two years without any effective remedy or recourse," Amnesty said in the report.
"Others have been released without explanation or apology or reparation after months in detention, victims of a system that is arbitrary and a recipe for abuse."
But the US military said each detainee is given a form explaining the reasons for their imprisonment and their files are reviewed every 90 to 120 days.
The Amnesty report called for an overhaul of the way detainees are treated by British, American and Iraqi authorities.
In particular, Amnesty International wants those who detain people in
Iraq to ensure inmates are given due process, a lawyer and an appearance before an impartial court, and to fully investigate any abuse allegations.
Quoting a US military Web site, the report said that figures compiled in November showed the number of detainees in coalition military prisons in Iraq was 14,000.
Last year, the US military said it planned to spend about $US50 million ($A67.25 million) to expand prison capacity to hold up to 16,000 people.
Controversial photographs from 2003 showing Iraqi inmates being abused led to the convictions of several US soldiers and major inquiries by US authorities into how prisoners are treated.