Reporting from Baghdad

Hundreds of Sunni men disappeared for months into a secret Baghdad prison under the jurisdiction of Prime Minister Nouri Maliki's military office, where many were routinely tortured until the country's Human Rights Ministry gained access to the facility, Iraqi officials say.

The men were detained by the Iraqi army in October in sweeps targeting Sunni groups in Nineveh province, a stronghold of the group Al Qaeda in Iraq and other militants in the north. The provincial governor alleged at the time that ordinary citizens had been detained as well, often without a warrant.

Worried that courts would order the detainees' release, security forces obtained a court order and transferred them to Baghdad, where they were held in isolation. Human rights officials learned of the facility in March from family members searching for missing relatives.

Revelation of the secret prison could worsen tensions at a highly sensitive moment in Iraq. As U.S. troops are withdrawing, Maliki, a Shiite Muslim, and other political officials are negotiating the formation of a new government. Including minority Sunni Arabs is considered by many to be key to preventing a return of widespread sectarian violence. Already there has been an increase in attacks by Al Qaeda in Iraq, a Sunni extremist group.

The alleged brutal treatment of prisoners at the facility raised concerns that the country could drift back to its authoritarian past.

Commanders initially resisted efforts to inspect the prison but relented and allowed visits by two teams of inspectors, including Human Rights Minister Wijdan Salim. Inspectors said they found that the 431 prisoners had been subjected to appalling conditions and quoted prisoners as saying that one of them, a former colonel in President Saddam Hussein's army, had died in January as a result of torture.

"More than 100 were tortured. There were a lot of marks on their bodies," said an Iraqi official familiar with the inspections. "They beat people, they used electricity. They suffocated them with plastic bags, and different methods."

An internal U.S. Embassy report quotes Salim as saying that prisoners had told her they were handcuffed for three to four hours at a time in stress positions or sodomized.

"One prisoner told her that he had been raped on a daily basis, another showed her his undergarments, which were entirely bloodstained," the memo reads.

Some described guards extorting as much as $1,000 from prisoners who wanted to phone their families, the memo said.

Maliki vowed to shut down the prison and ordered the arrest of the officers working there after Salim presented him with a report this month. Since then, 75 detainees have been freed and an additional 275 transferred to regular jails, Iraqi officials said. Maliki said in an interview that he had been unaware of the abuses. He said the prisoners had been sent to Baghdad because of concerns about corruption in Mosul.

"The prime minister cannot be responsible for all the behavior of his soldiers and staff," said Salim, praising Maliki's willingness to root out abuses. Salim, a Chaldean Christian, ran for parliament in last month's elections on Maliki's Shiite-dominated list.

Maliki defended his use of special prisons and an elite military force that answers only to him; his supporters say he has had no choice because of Iraq's precarious security situation. Maliki told The Times that he was committed to stamping out torture -- which he blamed on his enemies.

"Our reforms continue, and we have the Human Rights Ministry to monitor this," he said. "We will hold accountable anybody who was proven involved in such acts."

But Maliki's critics say the network of special military units with their own investigative judges and interrogators are a threat to Iraq's fragile democracy. They question how Maliki could not have known what was going on at the facility, and say that regardless, he is responsible for what happened there.

"The prison is Maliki's becauseit's not under the Ministry of Defense, the Ministry of Justice or Ministry of Interior officially," said one Iraqi security official, who spoke on condition of anonymity because of the sensitivity of the topic.

The revelations echoed those at the beginning of Iraq's sectarian war. In late 2005, the U.S. military found a secret prison in an Interior Ministry bunker where Sunnis rounded up in police sweeps were held.

The latest episode, the U.S. Embassy report warns, could exacerbate tensions between Iraq's Shiite majority and Sunnis even with the facility closed.

U.S. troops already have pulled out of Iraq's cities, and Iraqi officials say U.S. influence is diminishing as the Americans focus on ending their military presence. The number of U.S. troops in Iraq is scheduled to drop by about half, to 50,000, by the end of August.

The embassy report cautions that "disclosure of a secret prison in which Sunni Arabs were systematically tortured would not only become an international embarrassment, but would also likely compromise the prime minister's ability to put together a viable government coalition with him at the helm."

Maliki's main political rival, Iyad Allawi, narrowly defeated him in parliamentary elections last month. Allawi, a secular Shiite, drew on dissatisfaction in Sunni regions around central Iraq. In the interview, Maliki invited Allawi to join him in forming a new government. But news of a secret prison that falls under the jurisdiction of the prime minister's military office could make it difficult for him to gain any Sunni partners.

The controversy over the secret prison, located at the Old Muthanna airport in west Baghdad, has also pushed Maliki to begin relinquishing control of two other detention facilities at Camp Honor, a base in Baghdad's Green Zone. The base belongs to the Baghdad Brigade and the Counter-Terrorism Force, elite units that report to the prime minister and are responsible for holding high-level suspects.

Families and lawyers say they find it nearly impossible to visit the Camp Honor facilities. The Justice Ministry is now assuming supervision of the Green Zone jails, although Maliki's offices will continue to command directly the military units.

The 431 detainees brought down from Nineveh were initially held at Camp Honor. Interrogations began after they were transferred to the prison at the Old Muthanna airport.

According to the U.S. Embassy report and interviews with Iraqi officials, two separate investigative committees questioned the detainees and abused them. During the day, there were interrogators from the Iraqi judiciary. In the late afternoon they came from the Baghdad Brigade.

The embassy report says that at least four of the investigators from the Baghdad Brigade are believed to have been indicted for torture in 2006. The charges against them at the time included selling Sunni Arab detainees held at a national police facility to Shiite militias to be killed.

In December, the Human Rights Ministry asked the judiciary to investigate Baghdad Brigade interrogators over allegations of torture at Camp Honor, but hasn't received an answer, Iraqi officials said.

With the secret facility at the old airport being shut down, and both Maliki and Salim, the human rights minister, hailing what they regard as progress, some Iraqis with knowledge of the security apparatus say they are worried that nothing will really change.

One former lawmaker with great knowledge of the prime minister's security offices called for radical change in the next government. "This is the beginning. We have to hold people accountable," the former lawmaker said. "It's a coverup of torture."

ned.parker@latimes.com