In November, US soldiers said they found 173 incarcerated men in a secret interior ministry bunker, some of them emaciated and showing signs of torture.
Bayan Baqir Solagh Jabir, the Iraqi interior minister, played down the findings at the time, saying a handful of people had merely been beaten.
Since then, at least six joint US-Iraqi inspections have found abused detainees in several other detention centres, the Washington Post reported on Monday.
A US official involved in the inspections said the Iraqi detainees had "numerous bruises on the arms, legs and feet".
"A lot of the Iraqis had separated shoulders and problems with their hands and fingers too. You could also see strap marks on some of their backs," he said.
The abused captives found during the November 13 raid were transferred to a separate detention centre to protect them from further harm, but most detainees at centres subsequently inspected were not.
According to US and Iraqi inspectors, only a few of the most severely abused detainees at a one site were removed for medical treatment.
Prisoners at two other sites were removed to alleviate crowding. US and Iraqi authorities left the rest where they were, the Post said.
"There were several cases of physical abuse ... These included evidence of scars, missing toenails, dislocated shoulders, severe bruising, and cigarette burns"
spokesman for US detention operations
Lieutenant-Colonel Kevin Curry, the spokesman for US detention operations, said people that were transferred for medical treatment had "broken bones, indications that they had been beaten with hoses and wires, signs that they had been hung from the ceiling, and cigarettes burns".
"There were several cases of physical abuse at one other inspection site. These included evidence of scars, missing toenails, dislocated shoulders, severe bruising, and cigarette burns," he added.
"At the time of the inspection, most of the apparent injuries were months old. However, there were indications that three cases of abuse occurred within a week of the inspection. No detainee required immediate hospitalisation for injuries at that site."
The Post said that Curry's statement confirmed abuse depicted in photographs it had been given earlier by the US and Iraqi inspectors.
The failure to remove detainees from centres where there were well-documented cases of abuse has raised questions about whether the US was honouring a pledge by General Peter Pace, the chairman of the Joint Chiefs of Staff.
Pace said at a news conference on November 29, soon after the US soldiers discovered the first batch of abused detainees at an interior ministry secret bunker, that US troops would try to stop inhumane treatment if they saw it.
"It is absolutely the responsibility of every US service member, if they see inhumane treatment being conducted, to intervene to stop it," Pace said.
Fear of reprisal
An Iraqi official familiar with the joint inspections said that detainees who were not moved to other facilities were vulnerable.
"They tell us, 'If you leave us here, they will kill us'," he said on condition of anonymity because, he said, he and other Iraqis inspectors have received death threats.
Abdul Hussein Shandal, the Iraqi justice minister, said the Americans "don't have the right" to transfer detainees from detention centres operated by Iraqi ministries.
The November 13 raid "was the last incident in which the US asked for such a transfer", he said.
General John Gardner, the commander of US detention operations in Iraq, said in an interview: "I would strongly disagree with the statement that Americans are seeing cases of abuse and not doing anything."
The Washington Post observed that "the issue goes to the heart of US relations with the Iraqi government, which is led by Shia religious parties".
It said the interior ministry, "whose forces are overwhelmingly Shia, has been accused by Sunni Arabs and US officials of operating death squads that target Sunni men".
The paper also said the ministry's security forces had been "accused of deferring to militias belonging to the Shia religious parties, from whose ranks many of Iraq's police commandos and other ministry forces are drawn".
The Iraqi and US inspectors quoted by the Post both said that the prisoners were being held by the Wolf Brigade, "one of the interior ministry commando forces most feared by Sunnis".
The inspectors visited an interior ministry detention centre in Baghdad, a defence ministry site near the Green Zone, an interior ministry site in the city of Kut, an interior ministry site in the Muthanna neighbourhood of Baghdad and a "maximum crimes facility" in Baghdad.
The United States, some of whose troops have also been involved in abusing Iraqi prisoners, said it would inspect all of Iraq's more than 1,000 detention centres.