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 on the sprawling district.

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.