The International Red Cross had warned American officials for months that Iraqi prisoners were being abused in American-run prisons.
Earlier drafts found no systemic abuse at American-run prisons in Iraq or Afghanistan, and officials said that had not changed in the final report.
Voting centers were also set up in the American-run prisons at Abu Ghraib and Camp Bucca for some 13,000 detainees, many of them suspected insurgents.
Human Rights Watch says it has identified nearly 40 men and women who have disappeared into secret American-run prisons.
But American-run prisons hold only a small portion of Iraq's detainees.
Military officials said they had a tentative target of turning over American-run prisons to the Iraqis by the end of 2006, although no exact timetable has been approved.
The influx of detainees has swelled the population at the major American-run prisons to 119 percent of their ideal capacity, General Gardner said.
The senior official said it saved manpower and money, compared with keeping them in the United States or at American-run prisons abroad.
The United States military announced that it released about 50 male detainees from American-run prisons on Sunday.
At some American-run prisons in those countries, nudity among prisoners, both in cells and in interrogation rooms, was common, according to soldiers and Red Cross monitors.