Ambassador Zalmay Khalilzad told reporters that "over 100" of the 173 prisoners found last month in an Interior Ministry building in Baghdad's Jadriyah district had suffered abuse.
U.S. and Iraqi authorities visited a separate ministry lockup Thursday and found another 21 to 26 prisoners who had been abused, Khalilzad said.
"I want to let the Iraqi people know that we are very committed to looking at all of the facilities," Khalilzad said. "This is unacceptable for this kind of abuse to take place."
The Iraqi Human Rights Ministry said this week that 13 prisoners found at the second facility needed medical treatment.
Sunni Arabs long have complained about abuse and torture by Interior Ministry security forces, allegations that have become a major issue for Sunni Arabs in national parliamentary elections set for Thursday. Some Shiite politicians have suggested that American attention to the torture charges is aimed at getting out the Sunni Arab vote.
Interior Minister Bayan Jabr has said torture allegations have been exaggerated by people who sympathize with the Sunni-led insurgency.
Khalilzad said U.S. military officers would be joining Interior Ministry forces on counterinsurgency raids "so that they can observe ... how raids are carried out, how people are taken into custody."
After the discovery of the prisoners at Jadriyah, Prime Minister Ibrahim al-Jaafari, a Shiite, ordered an investigation and said a full report would be completed within two weeks. No report has yet been released, and Sunni politicians have accused the government of delaying it until after the election.
At a luncheon Tuesday for a group of Iraqi and Western reporters, al-Jaafari said he was deeply concerned about the abuse allegations.
"This government did not and will not allow the practice of torture even against the most hardened of criminals who committed crimes in all parts of Iraq," al-Jaafari said.
Al-Jaafari also suggested that it was unrealistic to expect the abusive practices and human rights violations to disappear quickly after decades of tyranny by Saddam's Baath party.