The clashes broke out after Iraqi national guardsmen raided al-Hanifa mosque in Baghdad's Adhamiya neighbourhood following Friday prayers, hospital sources said.
"We have received two killed and nine wounded, eight of them in serious condition," Amin Lamin of Al-Numan hospital said.
Al-Hanifa, considered one of the most important Sunni Muslim mosques in Iraq, has already been raided several times by US forces in recent months.
After prayers, about 200 to 300 national guardsmen stormed the mosque, throwing sound grenades and firing shots into the air.
The purpose of the raid was not immediately clear but some worshippers, gathered outside the mosque, said the security forces had arrested the mosque's imam, Shaikh Muayid al-Adhami.
Soon afterwards, US forces arrived and entered the mosque to post soldiers on the roof. Women were allowed to leave but men were kept inside.
Dozens of the mosque's guards were forced to lie on the ground by the US troops.
During his sermon, the imam had charged that after their devastating onslaught on the city of Falluja in western Iraq, US forces would target Latifiya.
Falluja toll disputed
Meanwhile, US military sources and the Falluja Mujahidin Council disputed the number of fatalities and casualties in the assault on the city, which entered its 11th day on Friday.
US soldiers said they destroyed
munitions used by the resistance
US press releases pointed to at least 51 US soldiers and marines killed and at least 425 wounded. The number of killed Iraqi National Guard was put at six with another 45 wounded.
The Mujahidin Council, however, said it killed nearly 400 US servicemen and another 145 of the Iraqi National Guard. It also claimed to have captured 126 US servicemen.
There has been no independent confirmation of either set of figures.