BAGHDAD, Iraq, May 23 — Even in a country beset by murder and death, the 16th Brigade represented a new frontier.

The brigade, a 1,000-man force set up by Iraq's Ministry of Defense in early 2005, was charged with guarding a stretch of oil pipeline that ran through the southern Baghdad neighborhood of Dawra. Heavily armed and lightly supervised, some members of the largely Sunni brigade transformed themselves into a death squad, cooperating with insurgents and executing government collaborators, Iraqi officials say.

"They were killing innocent people, anyone who was affiliated with the government," said Hassan Thuwaini, the director of the Iraqi Oil Ministry's protection force.

Forty-two members of the brigade were arrested in January, according to officials at the Ministry of the Interior and the police department in Dawra.

Since then, Iraqi officials say, individual gunmen have confessed to carrying out dozens of assassinations, including the killing of their own commander, Col. Mohsin Najdi, when he threatened to turn them in.

Some of the men assigned to guard the oil pipeline, the officials say, appear to have maintained links to the major Iraqi insurgent groups. For months, American and Iraqi officials have been trying to track down death squads singling out Sunnis that operated inside the Shiite-led Interior Ministry.

But the 16th Brigade was different. Unlike the others, the 16th Brigade was a Sunni outfit, accused of killing Shiites. And it was not, like the others, part of the Iraqi police or even the Interior Ministry. It was run by another Iraqi ministry altogether.

Such is the country that the new Iraqi leaders who took office Saturday are inheriting. The headlong, American-backed effort to arm tens of thousands of Iraqi soldiers and officers, coupled with a failure to curb a nearly equal number of militia gunmen, has created a galaxy of armed groups, each with its own loyalty and agenda, which are accelerating the country's slide into chaos.

Indeed, the 16th Brigade stands as a model for how freelance government violence has spread far beyond the ranks of the Shiite-backed police force and Interior Ministry to encompass other government ministries, private militias and people in the upper levels of the Shiite government.

Sometimes, the lines between one government force and another — and between the police and the militias — are so blurry that it is impossible to determine who the killers are.

"No one knows who is who right now," said Adil Abdul Mahdi, one of Iraq's vice presidents.

The armed groups operating across Iraq include not just the 145,000 officially sanctioned police officers and commandos who have come under scrutiny for widespread human rights violations. They also include thousands of armed guards and militia gunmen: some Shiite, some Sunni; some, like the 145,000-member Facilities Protection Service, operating with official backing; and some, like the Shiite-led Badr Brigade militia, conducting operations with the government's tacit approval, sometimes even wearing government uniforms.

Some of these armed groups, like the Iraqi Army and the Iraqi police, often carry out legitimate missions to combat crime and the insurgency. Others, like members of another Shiite militia, the Mahdi Army, specialize in torture, murder, kidnapping and the settling of scores for political parties.

Reining in Iraq's official and unofficial armies is the most urgent task confronting Iraq's new leaders. In speeches and private conversations, Prime Minister Nuri Kamal al-Maliki says he intends to clamp down on the death squads operating within the Iraqi government, and to disarm the militias that provide the street muscle for Iraq's political parties.

That presages an enormous political battle, one that extends beyond the Interior Ministry's police officers and paramilitary soldiers.

A larger and possibly more decisive struggle looms to disarm myriad other armed groups, including the Shiite militias, most of them answerable to the Shiite political parties that dominate the new government.

The outcome of the struggle has far-reaching implications for Iraq's future, as Iraqi and American officials try to curb the abuses that threaten to push the country closer to a sectarian war without impeding the government's ability to fight the Sunni-led guerrilla insurgency.

"I think they have the evidence now as to who is doing most of the killing," said an American official in Baghdad who is not authorized to speak publicly. "It's a question of political will, the political will to do what needs to be done."

"I have just not seen it yet," the official said.

Tales of Uniformed Killers

Every week, mothers and wives from Baghdad's Sunni neighborhoods stream into the makeshift human rights office at the Iraqi Islam Party, bearing tales of torture, kidnapping and murder at the hands of government security forces.

Most of the tales unfold in a grimly similar way: a group of Iraqis wearing official uniforms showed up at the house of a Sunni family and took away a young man. The family found his body a few days later, tossed into a ditch or laid out at the city morgue.

"It's the Ministry of Interior," said Omar al-Jabouri, who runs the Islamic Party's human rights office. Some of Iraq's new leaders, including its Sunni vice president, Tariq al-Hashemi, are calling for a wholesale purging of the Interior Ministry, saying there are "thousands" of corrupt and brutal officers who need to be fired if the government ever hopes to secure the trust of Iraq's Sunnis.

"You ask me who is doing these things," Mr. Hashemi said. "The police, the militias, the political parties — we don't know. But some of these people are criminals. In the Sunni areas, there is no confidence in them at all."

It is impossible to know just how many rogue units exist among the 145,000 police officers, commandos and other officers operating out of the ministry, most of them trained under American supervision.

That uncertainty lies at the heart of the political struggle that is now shaping up in Baghdad: Sunni and Shiite leaders disagree fundamentally on the nature and scope of the problem itself, which makes it harder to solve.

Leaders of the Shiite coalition, the largest partner in the new government, say the protests about the security forces, as well as their own militias, are being exaggerated for political effect. They say they plan to resist any wholesale transformation of the Interior Ministry.

Car bombings and suicide attacks have markedly dropped in Baghdad over the past several months, and the Shiite leaders say a large-scale purge of the Interior Ministry, or a rehiring of officers fired after the fall of Saddam Hussein, would probably revive the insurgency.

"A lot of noise comes from the fact that they are doing their jobs," Mr. Mahdi, the Shiite vice president, said of the Iraqi security forces. "We are in a war."

Indeed, to Iraq's main Shiite leaders, complaints about the Interior Ministry distract from the far larger problem of Sunni death squads, consisting of people whom they refer to as "taqfiris," the Arabic word that describes someone who hunts down apostates and violators of the faith. It has come to be a shorthand for insurgents who kill Shiites. In this formulation, the Shiite-dominated Interior Ministry is merely doing to Sunni insurgents what Sunni insurgents have been doing to the Shiites since April 2003.

"The problem is the Saddamists and the taqfiris," said Abdul Aziz Hakim, the leader of the Supreme Council for the Islamic Revolution in Iraq, one of the main Shiite parties that controls the government. "These groups are committing genocide against the Shiite people."

Rogue Units Suspected

Bayan Jabr, who until Saturday served as interior minister, hears the complaints about his forces and dismisses them with a wave of the hand.

"It's only rumor," Mr. Jabr said with a smile.

With a quick laugh and a fondness for powder-blue leisure suits, Mr. Jabr hardly seems a diabolical figure. A businessman and former newspaper editor, he portrays himself as a humble man thrust into a distasteful job.

"I'm not interested in occupying this job for myself," Mr. Jabr said. "This job does not suit my nature. Anything related to trade or business would be much better."

It was Mr. Jabr who presided over the rapid growth of the Iraqi security forces, and he has been the target of much of the criticism from Sunni leaders. He is a senior member of the Supreme Council for the Islamic Revolution in Iraq, which oversees its own militia, the Badr Brigade. He was once one of the brigade's commanders.

Upon taking the helm of the Interior Ministry last spring, he purged more than 170 employees who had been hired by the previous, more secular-minded Iraqi government. And he brought the first of thousands of Badr gunmen into the ranks of the police.

The Sunnis accused Mr. Jabr of allowing the largely Shiite police force to run wild in Sunni neighborhoods. American officials thought that was an exaggerated view of Mr. Jabr; they described him as a well-intentioned man who lost control of his ministry. For example, they point out, hundreds and possibly thousands of gunmen from the Mahdi Army militia, a rival to Mr. Jabr's Badr Brigade and loyal to the renegade cleric Moktada al-Sadr, also joined the police forces across the country.

While acknowledging the well-publicized cases of murder and torture within the Interior Ministry, American officers say that most of the atrocities are being carried out by a small number of rogues inside the government, or by groups, like the militias, that are not under Iraqi government control.

"The size of the problem is basically within a couple of brigades," said a senior American official, speaking on the condition of anonymity, citing the delicacy of the subject.

The official, who works closely with the Iraqi government, said he believed there was one group inside the Interior Ministry that was responsible for many of the atrocities: the 28th Battalion, whose official assignment is to provide security for the ministry itself.

The American official did not specify which atrocities he believed the battalion was responsible for. "We are very concerned about it," the official said. "They form the core of the death squads."

The official was reluctant to go into detail. American and Iraqi leaders agree that the subject of rogue elements operating inside the ministry is a delicate topic, particularly since they are trying to bring Sunni leaders into the government. Some declined to talk about the 28th Battalion, while others, like Mr. Jabr, said they had not heard of it.

In an interview in his Green Zone office before his new appointment as finance minister on Saturday, Mr. Jabr seemed eager to prove that he was in command of his ministry; at one point, he passed around a photo book containing the confessions of insurgents. They were all Sunnis.

According to Mr. Jabr, forces under the control of the Interior Ministry cover only about 25 percent of Baghdad; the Iraqi Army and American army cover the rest.

"Why are we just talking about MOI?" Mr. Jabr said. "The issue is fighting terrorists. We are just a small part of those who are battling them."

Indeed, the possibilities for government-sponsored violence are enormous: aside from the police and commandos in the Interior Ministry, approximately 117,000 soldiers are trained and equipped in the Iraqi Army. There are more than 50,000 private security guards, most of them armed, roaming the country. Another 145,000 men are assigned to protect Iraq's infrastructure.

Each of these units, Mr. Jabr said, could be infiltrated by insurgents or commit atrocities against Iraqi civilians, with few people in the senior levels of the government ever being aware.

"I am not responsible for these people," Mr. Jabr said of the other Iraqi forces. "You can imagine. This is out of my control. Out of control."

Mr. Jabr offered an example: two weeks ago, his men arrested a team of bodyguards protecting a person whom Mr. Jabr would describe only as a "very senior Iraqi official." The bodyguards, Mr. Jabr said, were using their government identification cards and official positions to run a kidnapping ring and death squad.

The senior Iraqi official, Mr. Jabr said, apparently did not know what his bodyguards were up to. "They said, 'We sent him home,' referring to their boss, 'and then we do our job.' "

Mr. Jabr said criminals and terrorists often impersonated police officers, wearing uniforms that can be bought at bazaars.

One woman, interviewed in the Baghdad neighborhood of Ur, said a group of eight men wearing Iraqi Army uniforms pulled into a side street near her home and parked their two cars, a black sport utility vehicle and white sedan, earlier this month. From the back of the S.U.V., the woman said, the men in army uniforms hauled out a blindfolded passenger, who appeared to be still alive, and moved him to the trunk of the sedan. Then the men shed their uniforms, tossed them into the vehicles and drove away.

The woman, whose name was not made public to protect her from possible retribution, said she never saw the men again.

"They were terrorists," the woman said. "It's such a terrible situation."

Ministries' 'Little Armies'

Where Sunnis point to the Interior Ministry, Shiite leaders are indignant about the Facilities Protection Service, a 145,000-man force spread throughout 27 Iraqi ministries, each with its own agenda. The officers, Iraqi officials say, are at the disposal of each minister.

"Now, in every ministry, there are 7 to 15,000 men who carry weapons and official identification cards," said Mr. Hakim, the Shiite leader. "They are under the command of the ministries. Some of them have committed many crimes."

One of the largest forces is assigned to the Oil Ministry, which maintains 20,000 troops to protect refineries and other parts of the country's oil infrastructure.

According to the force's director, Mr. Thuwaini, the first 16,000-member paramilitary police force was cobbled together in a haphazard way by a British-based consulting firm that neither trained the men nor checked their backgrounds for criminal records or ties to Mr. Hussein's security services.

"The British company hired people randomly, without training — they were profiteers," said Mr. Thuwaini, a Shiite civil servant not affiliated with any of the major parties. He took over the oil protection force in July 2005. "That is what we are trying to survive now."

The Facilities Protection Service was first set up in 2003 with only 4,000 men to protect crucial parts of Iraqi utilities like power plants and oil refineries. As insurgents stepped up their attacks, and the Americans needed to free up their troops for combat, the service was rapidly expanded. From August 2004 to January 2005, the number of the service's men grew to 60,000 from 4,000.

The man who oversaw that expansion was B. J. Turner, a 64-year-old consultant from Florida. Mr. Turner said he was the lone American assigned to the effort for the first several months. Facilities Protection Service guards received just three days of training and half the pay of regular police officers. They had no power of arrest.

"We actually trained people at times, firing one to two rounds, "Mr. Turner said. "Because that's all the ammunition we had."

Once the ministries starting paying their salaries, Mr. Turner said, the individual F.P.S. units became "little armies," loyal to the ministers who paid them.

Last month, an inspector general assigned to check American programs in Iraq released an audit of the $147 million F.P.S. program. The report said the auditors were never able to determine basic facts like how many Iraqis were trained, how many weapons were purchased and where much of the equipment ended up.

Of 21,000 guards who were supposed to be trained to protect oil equipment, for example, probably only about 11,000 received the training, the report said. And of 9,792 automatic rifles purchased for those guards, auditors were able to track just 3,015.

The Americans exercise no oversight over the F.P.S., nor does any central authority in the Iraqi government.

Oil Pipelines at Risk

As much as Mr. Thuwaini despairs over the men under his command, he saved his fiercest criticism for the pipeline protection units run by the Ministry of Defense. One of those units was the 16th Brigade, which he and other Iraqi officials said was operating as a death squad in Dawra.

Mr. Thuwaini said there were at least three other such brigades operating in Iraq that were also similarly out of control: the 9th, 10th and 11th Brigades of the Ministry of Defense's pipeline protection forces. Those three groups, Mr. Thuwaini said, appear to be cooperating with insurgents, regularly allowing oil pipelines to be destroyed.

Maj. Gen. Mahdi al-Gharawai, a senior official at the Interior Ministry, said he had no specific information on the 9th, 10th or 11th Brigades. But he said the Iraqi units assigned to guard the oil pipelines were widely regarded as useless. "Most of these oil pipeline protection brigades are corrupt and have ties to the insurgents," General Gharawai said.

Among the responsibilities assigned to Mr. Thuwaini's men is the protection of the oil refinery in Dawra. That, Mr. Thuwaini said, was a good thing.

"If those guys guarded the refinery," he said of the Ministry of Defense pipeline units, "it would be sabotaged every day."

Curbing the violence in Iraq, American officials say, means shutting down the private militias that roam the streets of most cities. That includes the Badr Brigade and the Mahdi Army, both allied to the Shiite-led government.

American and Iraqi officials say they believe that the Badr Brigade is responsible for killing hundreds, and possibly thousands, of Baathists after the fall of Mr. Hussein. The militia was set up in the early 1980's and trained in Iran, where many Shiite leaders were forced into exile during Mr. Hussein's rule.

The Mahdi Army, an informal militia that emerged after the American invasion to support Mr. Sadr, has engaged in two armed uprisings against the Americans and the Iraqi governments they backed.

Shortly after invading Iraq, the Americans outlawed the militias, but, despite many pledges to do so, they never disarmed them.

Now Shiite politicians say they need the militias to protect themselves from the insurgency. When the Shiite-led coalition first took power last spring, Mr. Hakim, whose party controls the Badr Brigade, publicly announced that it would carry on.

These days, the Mahdi Army is the most fearsome of the Shiite militias: after the bombing of the Askariya Shrine in Samarra in February, the militia's black-suited gunmen poured into Baghdad's mixed neighborhoods and killed hundreds of Sunnis. Through most of those chaotic days, the American military and the Iraqi police did nothing to stop them.

Militiamen or Policemen?

But confronting the Shiite militias head-on is a delicate and difficult task.

The two — government security forces on one hand, private militias on the other — are often indistinguishable. Many of the militiamen-turned-policemen, wearing Iraqi uniforms and driving Iraqi vehicles, carry out operations at the behest of their old commanders, sometimes after work.

Take, for instance, the case of Saud Abdullah Obeid, a 47-year-old Sunni man who disappeared from his Baghdad home last fall. According to his family, Mr. Obeid was taken away by a group of men wearing Iraqi commando uniforms and driving trucks bearing Interior Ministry insignia.

Shortly after Mr. Obeid was taken, the family said, they were contacted by members of the Mahdi Army, who demanded a ransom for Mr. Obeid's release. Iraqi officials told the family that Mr. Obeid was being held at the Mustafa Husseiniya, a Mahdi Army stronghold near Sadr City.

Mr. Obeid's relatives said they borrowed $50,000 from friends and turned it over to a middleman to deliver to the Mahdi Army. Mr. Obeid never came home. Instead, his body turned up in the city morgue, burned with acid and shot twice in the mouth.

"I can tell you, this government is the Mahdi Army," said Abdullah Obeid, the surviving son. "The government did this."

Late last year, a senior American commander said, American soldiers captured Mahdi Army fighters dressed in Iraqi police uniforms, carting away prisoners in Iraqi police cars to be tried in front of one of the Mahdi Army's Shariah courts, which operate independently of the government and deliver a harsh brand of Islamic justice.

"There are extremist elements of Badr and of the Mahdi Army who are using their positions in the police to carry out operations against the Sunni population," said a senior American military officer, who spoke on the condition of anonymity.

A Test of Political Will

Mr. Maliki, the new Iraqi prime minister, has taken the first small steps to control the militias. This month, the government decided to combine the different branches of the security forces in Baghdad to bring them under tighter control and curb the sectarian violence.

The key to Mr. Maliki's plan is a single uniform and a single identification card which, Iraqi leaders say, will allow them to spot private militiamen and rogue officers within the security forces.

Mr. Maliki also traveled to Najaf, the Shiite holy city, to persuade Grand Ayatollah Ali al-Sistani, the Shiite religious leader, to deliver a religious pronouncement against militias.

"Weapons should be carried only by government forces," Ayatollah Sistani said in his pronouncement. For all of his moral authority, though, it seems unlikely that the militias would disband merely at his command.

Mr. Maliki said he wanted to enforce a militia-demobilization law enacted by L. Paul Bremer III, who ran the Coalition Provisional Authority that ruled Iraq until June 2004.

But neither he nor subsequent Iraqi governments carried it out. The Bremer plan calls for militia fighters to be dispersed across the security forces so that their old units and chains of command are broken up.

In January, American military commanders said they would deploy more than 2,000 military personnel to work directly with Iraqi officers on the job, a four-fold increase.

Disbanding the militias means confronting the parties that control them, and the parties control the government. The Supreme Council, which controls the Badr Brigade, has 30 seats in the new Parliament; Mr. Sadr, who controls the Mahdi Army, has 31 seats.

Both parties appear to be reluctant to disband their forces, if only because of the inability of the government to guarantee their safety.

"We don't think the problem in Iraq is militias," Mr. Mahdi, the vice president, said. "People have to defend themselves."

In the end, whether the Iraqi government and their American backers are able to rein in the security forces will probably depend, more than anything, on political will. On that point, the Iraqis and the Americans appear to diverge.

Some American commanders say that a confrontation with Mr. Sadr and his militia is probably inevitable. Very few Iraqi leaders publicly agree.

Yet the dilemma for the Americans and the Iraqis seems clear enough. Without confronting Mr. Sadr, there seems to be little prospect of cleaning up the police force or the Mahdi Army. But, having faced two armed uprisings by Mr. Sadr in the past, the Americans hardly seem eager to incur the political fallout that another uprising would bring.

For their part, the Americans, privately at least, are hoping the Iraqis will take the lead. But they are not holding their breath.

"They need to begin by setting examples," an American official in Baghdad said of the Iraqi government. "It is just very noticeable to me that they are not making any examples."

"None," the official said. "Zero."

John F. Burns, Qais Mizher, Khalid al-Ansary and Ali Adeeb contributed reporting from Baghdad for this article, and David Rohde from New York.