BAGHDAD (AP) – U.S. forces backed by attack aircraft killed at least 25 Shiite militia fighters north of Baghdad on Friday in an operation targeting a cell accused of smuggling weapons from Iran, the military said.

Iraqi officials, however, said American bombs killed civilians who rushed to help those injured in the initial airstrike and claimed the only ones armed in the neighborhood were locals trying to organize themselves against al-Qaida.

Three U.S. soldiers were killed in roadside bombings Friday – two in southeastern Baghdad and one in Salahuddin province north of the capital, the military said. The military also reported the death of a soldier shot Thursday in a southern section of Baghdad used by al-Qaida cells.

The new chairman of the Joint Chiefs of Staff, U.S. Navy Adm. Mike Mullen met Iraq’s prime minister on a visit to Baghdad on Friday and urged Iraqis to seize the opportunity of improved security.

“I see a tremendous amount of change and progress since I was here before,” Mullen told reporters after discussions with Prime Minister Nouri al-Maliki in the Iraqi capital. “But we still face significant challenges in progress and security.”

Al-Maliki said Iraq has witnessed positive changes “after confronting the terrorist organization of al-Qaida,” but he stressed the need for better weapons for Iraqi troops to enable them to take over security responsibilities so U.S.-led troops can go home.

The Shiite leader also expressed concern about U.S.-sponsorship of Sunni tribal councils that have turned against al-Qaida, demanding that they be accepted “within the framework of the law so that we do not allow the emergence of new militias and so that arms would be with the state, not with the party or the sect.”

In Friday’s pre-dawn raid in Khalis, a Shiite enclave about 50 miles north of Baghdad, gunmen opened fire on the soldiers with assault rifles and rocket-propelled grenades, and at least one man was carrying what appeared to be an anti-aircraft weapon, the military said. Ground forces called for air support when the fighters kept coming, the military said. Two buildings were destroyed in airstrikes, it said.

An Iraqi army official, who spoke on condition of anonymity because he was not authorized to release the information, said U.S. aircraft bombed the neighborhood repeatedly and he claimed civilians, including seven children, were among those killed and three children were among the 28 wounded.

He said the civilians were killed when families rushed out to help those hurt in the initial bombing.

The U.S. military said the raid was aimed at the commander of a rogue militia group believed to be associated with the Quds Force, an elite branch of the Iranian Revolutionary Guards.

But the town’s top official said U.S. forces targeted areas built up by locals to protect their Shiite neighborhood against attacks by al-Qaida gunmen. The guards were armed and worked around the clock, he said.

“These places came under attack by American airstrikes,” said Khalis Mayor Odai al-Khadran. “Locals were protecting themselves by guarding their village. They are not militias killing people.”

Since launching a Baghdad security crackdown more than seven months ago, U.S. troops have increasingly battled splinter groups from the country’s most powerful Shiite militia, the Mahdi Army. The Mahdi Army is nominally loyal to Muqtada al-Sadr, the radical cleric, who in August ordered a temporary freeze on his followers’ activities – including attacks on U.S. troops.

“We continue to support the government of Iraq in welcoming the commitment by Muqtada al-Sadr to stop attacks and we will continue to show restraint in dealing with those who honor his pledge,” Maj. Anton Alston, a U.S. military spokesman, said Friday. “We will not show the same restraint against those criminals who dishonor this pledge by attacking security forces and Iraqi citizens.”

Last month, the U.S. military arrested a man suspected of being a ranking officer of the Quds Force, the paramilitary branch of the Revolutionary Guards, which has been accused of arming Shiite militants in Iraq. Iran denies the charges.

The U.S. said the arrested Quds officer, Mahmudi Farhadi, was posing as a businessman.

In January, five other Iranians accused of being members of the Quds Force were arrested in a U.S. military raid in Irbil. They remain in U.S. detention. Iran says the men were in Iraq on official business.

The U.S. military said separately that it was investigating the deaths of three civilians who were shot by American troops near a checkpoint.

That investigation focused on a shooting Thursday in Abu Lukah, a village just north of Musayyib, about 40 miles south of Baghdad, the military said. The brief announcement did not identify the civilians by sect or provide other details.

But a local police spokesman said those killed were Shiite members of the North of Hillah Awakening Council, a group of Iraqis who have turned against extremists in the area.

Five council members were guarding a deserted road into their village at about 2 a.m. when U.S. troops fired on them from a watchtower at a nearby military base, the spokesman said, speaking condition of anonymity because he was not authorized to release the information. Three guards were killed, another was wounded and the fifth man fled on foot, the official said.

The U.S. military is relying heavily on the growing number of Sunni tribes that have turned against al-Qaida, saying their support is key to a secure Iraq. It also has been trying to extend the movement to Shiites opposed to growing lawlessness among militia factions.

The Americans point to successes in Anbar province, which is now largely peaceful after Sunnis joined the Iraqi military and police force as a way to both protect themselves from extremists and to empower them in the face of the Shiite-led central government in Baghdad.

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Associated Press correspondent Sinan Salaheddin contributed to this report.

AP-ES-10-05-07 1444EDT