The U.S. military says its forces "returned fire in self-defense" after coming under rocket-propelled grenade and machine gun fire from the building.
It says the mosque suffered serious structural damage to the dome and minaret. It is not immediately clear whether any insurgents were killed.
In other incidents of sectarian and insurgent violence has today claimed seven victims in areas across Iraq.
Five killings were reported in Diyala Province and its capital Ba'qubah, a mixed Sunni and Shi'ite region just north of Baghdad in which there are daily reports of operations by death squads and insurgent groups.
In Al-Nasiriyah, in the mainly Shi'ite south, two people were reported killed when members of the radical cleric Muqtada al-Sadr's militia clashed with fellow Shi'ites guarding a local mosque.