The forthright criticism of US tactics comes just days after the launch of a much-publicised American-Iraqi crackdown, supported by Mr Maliki, on sectarian Sunni-Shia violence in the capital. But in a statement on government television late on Monday night, Mr Maliki said he was "very angered and pained" by the latest operation, which involved air and ground forces in the volatile Sadr City area early in the morning.
"Reconciliation cannot go hand in hand with operations that violate the rights of citizens this way," Mr Maliki said.
The US military said the raid, which also involved Iraqi forces, had targeted "individuals involved in punishment and torture cell activities" and was part of an effort to stem the sectarian violence in Baghdad and avert a broader civil war.
The military said three people had been arrested but made no mention of fatalities. Residents reported a fierce firefight that lasted more than two hours.
"This operation used weapons that are unreasonable to detain someone, like using planes," Mr Maliki said. He apologised for the operation and vowed: "This won't happen again." He also sent an envoy to Sadr City to offer cash payments to families of the dead and wounded.
At the end of June, Mr Maliki unveiled a blueprint for national reconciliation. But neither that, nor a succession of security offensives, have halted the bloodshed in the capital. Four roadside bombs in Baghdad yesterday killed at least 19 people. The deadliest blast killed at least 10 and wounded 69 others in a central Baghdad market. Other bombs targeted police and a busy bus station. Two Iraqi journalists were reportedly killed in separate incidents in Baghdad.
The impoverished Sadr City district provides many of the footsoldiers for Mr Sadr's Mahdi army militia, which is widely suspected of conducting sectarian attacks against Sunnis.
Mr Maliki has vowed to restore security to the capital and rein in the militias but his task is complicated by the knowledge that some groups are linked to some of his main political allies. For example, since the Mahdi army staged two failed uprisings against coalition troops in 2004, supporters of the anti-western cleric have entered politics, forming a powerful bloc within Mr Maliki's ruling Shia alliance.
In an attempt to break up the death squads in Baghdad, US and Iraqi forces have staged a number of raids in Sadr City, but commanders have been at pains to point out the crackdown is not aimed at particular groups. With anger among Iraqi Shias already riding high owing to the Lebanon crisis Mr Maliki knows he can ill afford to further alienate Sadr supporters.
Abdul Jabbar, a political science professor at Baghdad University, said: "The prime minister is in a tricky position. He is under pressures from the Sadrists in his own alliance and at the same time from the Americans."
