Deputy head of the Higher Council for Propagation and Guidance, Shaikh Mahdi al-Sumaidi, told Aljazeera that up to 100 Iraqi police stormed the Ibn Taimiya mosque on Saturday morning.
In the "second incident" of its kind, al-Sumaidi said, contents of the mosque, such as furniture and Qurans, were thrown around during the raid.
He blamed "the interim Iraqi government and the former ruling council" for the raid, adding that "it came at their behest".
A US officer at the scene, Captain Tom Burrell, told AFP that "we received reports weapons were being stored in the mosque ... We came at 10.00 am (0600 GMT) and, with the full cooperation of the mosque's imam, we searched the mosque and found nothing."
The Iraqi contingent was backed by US armour. The US officer said only Iraqis entered the mosque, which lies beside the main highway leading to the airport.
US forces sealed off the area
around the Ibn Taimiya mosque
Al-Sumaidi reportedly denounced the operation as part of an effort to intimidate the group because it opposes the US military presence in Iraq.
He particularly condemned Iraqi security forces for working alongside the Americans.
"They have no respect toward a mosque," he is quoted as saying. "We know that the government has betrayed its people many times."