Global Policy Forum

In the weeks since the February bombing of a Shiite shrine in the town of Samarra, the militias and their allies in the Interior Ministry are thought to have been responsible for the deaths of hundreds, if not thousands, of Sunnis, who've been shot, hanged or tortured. The belated US effort to persuade Iraq's Shiite-led government to crack down on the militias is being met with resentment. Many Shiite leaders say the militias are an important defense against Sunni aggression.

"They forget that the Sunnis have been killing us for 45 years - for every action there is a reaction," said Abu Haider Lami, a senior official in the Badr Organization who used his nom de guerre during an interview at Badr offices in Baghdad. "What do they expect?" At the beginning of 2005, neither militia was nearly as powerful as it is today. Al-Sadr's men had been defeated twice during uprisings against the US military in 2004, and Badr was still operating largely outside the Iraqi security forces. L. Paul Bremer, then the top American official in Iraq, and then-Secretary of State Colin Powell wanted to destroy al-Sadr's Mahdi militia in 2004, but Pentagon officials and US military commanders balked, saying it was unwise to open a new battle with Shiite fighters at the same time the United States was concentrating on the Sunni insurgency.

In May 2005, the new Iraqi government appointed Bayan Jabr, a prominent member of the Supreme Council for Islamic Revolution in Iraq with close ties to Badr, to head the Interior Ministry, which oversees the nation's police and several specialized security units. Less than a month after the interim government took power, the bodies of Sunni clerics began turning up in Baghdad. Many bore signs of torture: cuts, bruises and holes apparently made by electric drills.

Al-Sadr's militia, meanwhile, underwent a reorganization in which its provincial offices were streamlined into a national council in Baghdad, giving Mahdi commanders much better tactical control of their men. As they regrouped, the Mahdi gunmen continued to exert considerable control in Sadr City, Baghdad's largest neighborhood and home to more than 2 million Iraqis. The killings continued into the summer. Sunni family members said the dead had been picked up by men wearing security forces uniforms and driving SUVs similar to Interior Ministry vehicles.

Iraqi politicians said they tried to get the Americans to intervene. They were met with sympathetic words but little action. "The American politicians couldn't understand the deepness and complications of the region," said Falah al-Nakib, the interior minister from June 2004 to April 2005, who said he raised the militia problem and the growing Iranian influence in Iraq with US Secretary of Defense Donald H. Rumsfeld. "They didn't take us seriously." Al-Nakib said the Americans seemed convinced last year that elections for an interim government in January 2005 and for a permanent government in December would lead the Shiite parties to curb the militias. Instead, the bodies of Sunnis continued to pile up.

US officials long have known that the Shiite militias could become a problem. Officials in Washington said alarms about the growing power of the militias began in late 2003 and were raised throughout 2004 and 2005 by a variety of agencies, including the CIA, the Defense Intelligence Agency and the US Embassy in Baghdad. Senior officials dismissed the reports as "nay-saying" and "hand-wringing," said two former senior officials in Washington who were responsible for Iraq policy through most or all of that period and one top official who remains in government. The officials agreed to speak only on the condition of anonymity because they discussed intelligence reports that remain classified.

In May 2004, Bremer, who headed the Coalition Provisional Authority, which then governed Iraq, formed a committee of high-ranking Iraqi officials who were to meet with militia leaders and persuade them to disband their groups. The next month, weeks before returning sovereignty to an interim Iraqi government, Bremer signed a law banning militias. The order enshrined the committee, known as the Transition Reintegration Implementation Committee, and named it as a key part of the disarmament process.

But no money was allocated to fund the committee's support offices, according to a US diplomat in Baghdad. That rendered it almost completely ineffective. "They were really never given any teeth," another American Embassy official said. The US Embassy agreed to allow interviews with the two American officials, both of whom have extensive knowledge of Iraq's militias, on the condition that they not be identified. Other officials showed little zeal to investigate militia activity, in spite of the growing evidence that they'd infiltrated Iraqi police commando units and were using their positions to kill Sunnis.

Asked last June about the possibility, Steven Casteel, a senior US adviser to the Interior Ministry, brushed the question aside. "The small numbers that we've investigated we've found to be either rumor or innuendo," he told Knight Ridder at the time. In July, a top Sunni politician, Saleh al-Mutlak, publicly accused Shiite militias of infiltrating the security forces and killing Sunnis involved with drafting the nation's constitution.

The arrival of Zalmay Khalilzad as US ambassador in Baghdad last summer brought renewed discussion of the militia threat. In one of his first news conferences, Khalilzad said America opposed militias. But there still were few signs of action as the Sunni death toll mounted. Sunni groups such as the Iraqi Islamic Party gathered the names of the dead. Hospital workers said Iraqi police often dumped off the bodies.

"We've lodged complaints with the prime minister, the Americans, the Human Rights Ministry ... and so far, there have been no results," Omar al-Jabouri, who heads the human rights section of the Iraqi Islamic Party, said during an interview earlier this month. The issue gained attention last November when American forces discovered more than 160 prisoners at a secret Interior Ministry bunker. Many had been beaten with leather belts and steel rods and forced to sit in their own excrement in tiny cells crammed with dozens of prisoners. Two police officers who had knowledge of the facility said Badr ran it.

The two US officials at the American Embassy in Baghdad were asked what steps the US mission in Iraq had taken before the bunker raid. One of them replied: "Nothing's jumping to my mind right off the bat." The official said allegations of Interior Ministry abuses were forwarded to the interior minister, Jabr, the man with close ties to the Badr militia. "We understand what his background is, but he is the minister of interior and he is ultimately responsible for these forces," the American official said. "Have we formed our own internal affairs unit to go out and investigate the Iraqi police? We haven't done that; that's not a function we would perform."

Adnan Ali, a top adviser to Prime Minister Ibrahim al-Jaafari, a Shiite, said there was a compelling reason the Americans didn't do more to address the militias in 2005: There weren't enough US and Iraqi troops to fight the insurgency while risking an uprising by tens of thousands of Shiites by cracking down on militias. Adnan Pachachi, the acting speaker of parliament and an elder Sunni statesman, said the Americans' inattention last year to such a complicated situation was easy to understand. "The so-called Sunni insurgency is active in hostilities toward the Americans, while Badr - and perhaps the Mahdi Army - is not attacking Americans; Badr has been rather careful not to antagonize the Americans, not to provoke them," Pachachi said. "I think it's natural that their first reaction would be toward those who are attacking them."

Leaders from the Supreme Council for Islamic Revolution in Iraq and al-Sadr's group blame the Americans for failing to reel in the Sunni insurgency and establish security. "I am against militias, but because of the situation in Iraq we need militias to protect us," said Transportation Minister Salam al-Maliki, a key al-Sadr political negotiator who deeply dislikes the US presence in Iraq. "America doesn't know anything about militias in Iraq; it hasn't come up with any solution for them."

John Walcott contributed to this report from Washington