The unrest reflected growing tension over the high unemployment rate in Iraq after the collapse of Saddam Hussein's military, formerly a major employer.
When Saddam's army was disbanded in May, the U.S.-led Coalition Provisional Authority decided to make one-time stipend of $40 to the estimated 440,000 conscripts in the former military.
The idea was to tide the soldiers over until new jobs for them were created. Saturday was the final day for collecting the payments, distributed at nine locations across the country.
U.S. officials said Sunday that more than 320,000 former Iraqi soldiers, or 72 percent, had benefited from the program and blamed Saddam loyalists for inciting the protests.
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Hundreds of men claiming to be former soldiers have gathered in Baghdad and Basra, the second largest city after the capital, over the past two days, angrily claiming they have not been paid. The weekend clashes left three rioters dead and dozens injured in the two cities. Coalition officials said two U.S. soldiers were injured.
Coalition spokesman Charles Heatley said some Iraqis were refused payment because they could not prove they had been in the military.
"We made payments right through 9:15 p.m. They had a list of conscripts entitled to pay. Those who came and were able to prove their ID received their payments," he said.
The protesters who "have come forward saying they should be paid are not on the list as far as we're concerned and they were not conscripts in the army."
Coalition officials say the violent demonstrations, instead, were being provoked by remnants of Saddam's Baath Party, some of whom were arrested on Saturday.
"It's absolutely clear to us that there were former, very senior Baathist officers, some who are now in custody, who were stirring up these crowds," Heatley said.
Many of the men at Sunday's protest in Baghdad voiced frustration and even desperation that they had no jobs and no money to support their families.
One man in a ragged black T-shirt screamed out, "Look at me. How will I pay rent? How will I feed my children?"
Trying to calm the crowd, police chief Gen. Hassan al-Obeidi told them to form a committee to discuss the matter with the authorities Monday.
The demonstrators dispersed peacefully after some pushing and shoving with U.S. soldiers and Iraqi police, unlike the day before when the crowd began hurling stones at the Americans and the Iraqi officers, who fired shots to try to disperse them.
Later Saturday some rioters moved to nearby Mansour district, where they burned and looted four liquor stores and set fire to an Iraqi police car in the upscale neighborhood.
Two ex-soldiers died from gunshot wounds to the head and at least 25 people were hurt during the Baghdad riot, according to hospital officials. U.S. officials said two soldiers were wounded and four Iraqis injured.
Heatley said the coalition administration is aware the high unemployment rate is creating huge tensions in the country, but that major job programs are underway. An irrigation program has put 100,000 people to work, while 100,000 public works jobs are being created in 11 of Iraq's 18 provinces, he said.
"We've taken a lot of steps to try to get the private sector going. It's clear to us that in the future, jobs will come from the private sector instead of the public sector," he said.
On Sunday, British troops in Basra, in the extreme south of the country, fired rubber bullets to disperse a crowd that was throwing stones at passing cars and setting tires on fire. Six of the group were arrested, Maj. Charlie Mayo said.
Mayo said the disturbance occurred after ex-Iraqi soldiers were notified earlier in the day that they would not be receiving their one-time stipend.
Mayo said the men were angry but dispersed after being informed that rioters at the stipend payment point a day earlier had burned the payment. British soldiers had killed one man during protests on Saturday.
Krivo said the circumstances of that death were still under investigation, adding that several sources reported seeing a man in civilian clothing crawling on a rooftop to get a shooting vantage point before he was shot.
Also on Sunday, U.S. troops raided the Tikrit home of a suspected weapons dealer, arresting him and seizing blasting caps and other materials often used by Iraqi insurgents to build the roadside bombs that target American soldiers.
During the raid, Apache helicopters hovered as troops backed by Bradley fighting vehicles battered down the front of the house, looking for a man identified by fellow Iraqis as a weapons dealer and possible member of the Fedayeen, the regime's former militia.
Inside, they found bomb-making materials and detained two people, including the suspected dealer. The raid took place near the site of an Oct. 1 roadside bombing that killed a woman soldier serving with the 4th Infantry Division.
U.S. troops have intensified their hunt for bomb makers and their bankrollers following a recent increase in roadside attacks against American convoys and patrols, which have killed seven soldiers from the 4th ID, based in Fort Hood, Texas, over the past three weeks.