BAGHDAD – The U.S. military said its forces killed an estimated 49 militants during a dawn raid to capture an Iranian-linked militia chief in Baghdad’s Sadr City enclave, one of the highest tolls for a single operation since President Bush declared an end to active combat in 2003.

Iraqi police and hospital officials, who often overstate casualties, reported only 15 deaths including three children. Iraqi government spokesman Ali al-Dabbagh said all the dead were civilians.

Al-Dabbagh said on CNN that Prime Minister Nouri al-Maliki, a Shiite, had met with the U.S. commander in Iraq, Gen. David Petraeus, to protest the action.

Associated Press photos showed the bodies of two toddlers, one with a gouged face, swaddled in blankets on a morgue floor. Their shirts were pulled up, exposing their abdomens, and a diaper showed above the waistband of one boy’s shorts. Relatives said the children were killed when helicopter gunfire hit their house as they slept.

One local resident said some of the casualties were people sleeping on roofs to seek relief from the heat and lack of electricity. The Iraqi officials said 52 were wounded in the raid.

The U.S. military said it was not aware of any civilian casualties, and the discrepancy in the death tolls and accounts of what happened could not be reconciled. American commanders reported no U.S. casualties.

The raid on the dangerous Shiite slum was aimed at capturing an alleged rogue militia chief, one of thousands of fighters who have broken with Muqtada al-Sadr’s mainstream Mahdi Army. The military did not say if the man was captured. He was also not named.

The Shiite cleric has ordered gunmen loyal to him to put down their arms. But thousands of followers dissatisfied with being taken out of the fight have formed a loose confederation armed and trained by Iran.

The U.S. operation was the latest in a series that have produced significant death tolls, including civilians, as American forces increasingly take the fight to Sunni insurgents, al-Qaida militants and Shiite militiamen.

The intensity and frequency of American attacks and raids have grown since the arrival of the last of 30,000 additional soldiers on June 15.

The reinforcements were ordered into Iraq earlier this year by Bush and have inflicted a heavy toll on militants on both sides of Iraq’s sectarian divide. American commanders credit the troop buildup for a sharp drop in the number of attacks and deaths of U.S. soldiers and Iraqi civilians, particularly in the past two months.

As U.S. forces pounded Sadr City, the potential grew for a fresh explosion of fighting on a new front, Iraq’s northern border with Turkey.

Early Sunday, Kurdish separatist rebels who take shelter in the rugged mountains on the Iraqi side of the frontier ambushed a military unit inside Turkey and killed at least 12 soldiers. Turkish forces responded by lobbing at least 15 artillery shells toward mainly abandoned Kurdish villages inside Iraq, according to Iraqi border guard Col. Hussein Rashid. He said there were no casualties.

In the Sadr City raid, the U.S. military said forces killed “an estimated 49 criminals” in three linked attacks during an intelligence-driven raid to capture the rogue Shiite kidnapper who was partially funded by Iran.

U.S. troops returned fire under attack from automatic weapons and rocket-propelled grenades from nearby buildings as they began raiding structures in the district, according to a statement. It said 33 militants were killed in the firefight. Ground forces then called in helicopter airstrikes, which killed six more militants.

As American soldiers left the zone, troops were hit by a roadside bomb and continued heavy fire, killing 10 more combatants.

“All total, coalition forces estimate that 49 criminals were killed in three separate engagements during this operation. Ground forces reported they were unaware of any innocent civilians being killed as a result of this operation,” the military said.

A local resident who goes by the name Abu Fatmah said his neighbor’s 14-year-old son, Saif Alwan, was killed while sleeping on the roof.

“Saif was killed by an airstrike and what is his guilt? Is he from the Mahdi Army? He is a poor student,” Abu Fatmah said.

An uncle of 2-year-old Ali Hamid said the boy was killed and his parents seriously wounded when helicopter gunfire pierced the wall and windows of their house as they slept indoors.

Relatives gathered at Sadr City’s Imam Ali hospital where the emergency room was overwhelmed with bloodied casualties. The dead were placed in caskets covered by Iraqi flags.

APTN video showed three bloodied boys sitting on hospital tables and an elderly man being treated for a head wound. Mourners tied wooden coffins onto the tops of minivans with a plume of smoke in the background. Other footage showed a U.S. helicopter flying over the area while black smoke rose.

The sweeps into Sadr City have sent a strong message that U.S. forces plan no letup on suspected Shiite militia cells despite objections from the Shiite-led government of al-Maliki, who is working for closer cooperation with Shiite heavyweight Iran.

An Iraqi military spokesman, Brig. Gen. Qassim al-Moussawi, said the government would ask the Americans for an explanation of Sunday’s raid and stressed the need to avoid civilian deaths.

The government has issued mixed reactions to the raids and airstrikes, particularly those that have targeted Sunni extremists.

U.S. troops backed by attack aircraft killed 19 suspected insurgents and 15 civilians, including nine children, in an operation Oct. 11 targeting al-Qaida in Iraq leaders northwest of Baghdad.

Al-Maliki’s government said those killings were a “sorrowful matter,” but emphasized that civilian deaths are unavoidable in the fight against al-Qaida in Iraq.