The US military denied damaging the shrine and said an air crew saw militants in the compound fire a rocket that clipped one of the walls and exploded 10 yards outside the compound.
"We are not doing anything that could have caused damage to the shrine," Marine Captain Carrie Batson said.
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There was no independent confirmation of damage to the shrine, but violence earlier yesterday ripped a chunk out of the outer wall of the compound. Explosions throughout the day shook the Old City, which is a mix of streets and narrow, maze-like alleys at the heart of much of the fighting.
With the US advance yesterday, fewer Sadr militiamen were in the streets, and some were seen leaving Najaf. Militant medical officials said at least two insurgents were killed and four wounded.
Al-Hakim Hospital said two civilians were killed and two others injured, but more casualties were reported in the Old City and could not be reached by emergency workers, said hospital employee Hussein Hadi.
Sadr, whose Mahdi Army fighters are behind the uprising, has not been seen in public for many days, and police drove around Najaf declaring on loudspeakers that he had fled toward Sulaymaniyah in northern Iraq. Sadr's aides denied that report.
"Moqtada al-Sadr is still in Najaf and is still supervising the operations," Sheik Aws al-Khafaji, the head of Sadr's office in the southern city of Nasiriyah, told Al-Jazeera television.
Worries that the violence could spread brought new calls yesterday from Iraq's neighbors and other Islamic countries for international intervention to end the fighting in Najaf.
In Baghdad's heavily Shi'ite neighborhood of Sadr City, which has been racked by violence since the Najaf uprising began, an explosion killed four people and injured nine, said Dr. Qasim Saddam, director of Sadr Hospital. The cause of the blast was unclear, and the US military said it was unaware of the bombing.
An American soldier was killed and two others were wounded when insurgents fired a rocket-propelled grenade at a patrol in Baghdad, the US military said yesterday.