Baghdad, Iraq ? A top deputy of Shiite cleric Muqtada al-Sadr was killed Wednesday during a raid by U.S. and Iraqi troops in the southern holy city of Najaf, sparking protests from al-Sadr’s followers and complicating an already tense relationship with the powerful anti-American leader.

Hurling rocks and shouting expletives, thousands of angry al-Sadr loyalists marched through the streets of Najaf after Sahib al-Amiri was shot and killed by an American soldier during an early morning raid. “Agents and stooges!” protesters shouted at Iraqi soldiers and local authorities.

U.S. military officials declined to confirm that al-Amiri was an al-Sadr aide, saying only that he had provided explosives for use against Iraqi and American forces. Al-Sadr officials said al-Amiri was an aide, and also a lawyer who ran an educational organization that helped orphans and impoverished children. They said he had no connections to illegal activity.

In a statement, the U.S. military said Iraqi and American forces were trying to detain al-Amiri, and only shot him when he pointed an assault rifle at an Iraqi soldier.

The incident comes at a delicate time for the Iraqi political process. Al-Sadr, who runs one of the country’s most feared militias, is also a potent political force; his allies control 30 seats in parliament and four key ministries. Last month, influential politicians linked with al-Sadr suspended their participation in the government to protest a meeting between Prime Minister Nouri al-Maliki and President Bush in Jordan. Unable to pass legislation without al-Sadr’s support, and fearing Iraq’s government could collapse, other Shiite leaders have been appealing for an to end to the boycott.

Bahaa al-Araji, a senior legislator with al-Sadr’s Shiite Muslim party, said discussions about a return to government were scheduled for Wednesday, but were delayed by al-Amiri’s death. “Because of this problem, we’ll leave everything for a few days,” he said.