The allegations, made by U.S. and Iraqi witnesses in a documentary produced by The Guardian and BBC Arabic, implicate U.S. advisers for the first time in human rights abuses committed by Iraqi commandos.
The report, published Wednesday, said the Pentagon sent a veteran of Central America's "dirty wars" to Iraq to direct sectarian police commando units that set up secret detention and torture centers in the early 2000s.
Col. James Steele, 58, a retired special forces veteran helped organize the paramilitaries to try to quell a Sunni insurgency, an investigation by the Guardian and BBC Arabic indicated.
Another adviser, retired Col. James Coffman, worked with Steele in the detention centers, The Guardian reported. Coffman reported directly to Gen. David Petraeus, deployed to Iraq in June 2004 to organize and train the new Iraqi security forces.
The documentary is the first time Petraeus -- who last November resigned as CIA director after admitting to an extramarital affair -- was linked through an adviser to the alleged abuse in Iraq.
Coffman and Steele "worked hand in hand," said Gen. Muntadher al-Samari, who worked with the two for a year while the commandos were being set up. "I never saw them apart in the 40 or 50 times I saw them inside the detention centers. They knew everything that was going on there ... the torture, the most horrible kinds of torture."
The Guardian article said no evidence indicated Steele or Coffman tortured prisoners, only that they sometimes were in the detention centers where torture occurred and were involved in processing detainees.
Samari described to The Guardian how the interrogation system worked.
"Every single detention center would have its own interrogation committee," Samari said. "Each one was made up of an intelligence officer and eight interrogators. This committee will use all means of torture to make the detainee confess like using electricity or hanging him upside down, pulling out their nails, and beating them on sensitive parts."
The Guardian-BBC Arabic investigation was prompted by release of classified U.S. military logs on WikiLeaks that detailed incidents in which U.S. troops found tortured detainees in detention centers operated by police commandos across Iraq. Army Pfc Bradley Manning pleaded guilty to leaking the documents to the whistle-blowing website.
Samari alleged that torture was routine in the detention centers.
"I remember a 14-year-old who was tied to one of the library's columns. And he was tied up, with his legs above his head," he said. "Tied up. His whole body was blue because of the impact of the cables with which he had been beaten."
A U.S. journalist and photographer said they saw blood on the floor of a library and heard screams of agony while at one of the centers interviewing Steele, The Guardian said.
Steele did not respond to a request for an interview from The Guardian and BBC Arabic. In the past, he has denied any involvement in torture and has said he is "opposed to human rights abuses."
Coffman declined to comment.
An official speaking for Petraeus said, "During the course of his years in Iraq, General Petraeus did learn of allegations of Iraqi forces torturing detainees. In each incident, he shared information immediately with the U.S. military chain of command, the U.S. ambassador in Baghdad ... and the relevant Iraqi leaders."
Gen. Adnan Thabit, the head of Iraq's special commandos, said, "Until I left, the Americans knew about everything I did; they knew what was going on in the interrogations and they knew the detainees."