The 7am (0400 GMT) mortar attack targeted the Ibn Taymiya Mosque in western Baghdad, sending plumes of smoke into the sky, shattering the mosque's windows and showering the building's carpeted floor with shards of glass.
The injured were taken to al-Yarmuk hospital.
Shaikh Fakhri al-Qaisi, secretary-general of the Supreme Association for Guidance and Dawa, told Aljazeera: "It is a deliberate attack because the two mortars hit the mosque and apparently were not fired aimlessly.
"This mosque and this association have been targeted since the beginning of the occupation, for more than 19 months, arresting its members almost every month," he said.
"The inside of the mosque has been severely damaged," he said.
"The association, through this mosque, one of the most prominent in Iraq, completely rejects the occupation of the country," al-Qaisi said.
"It has always stood against the conspiracies of the US-Zionist project," he added.
"The association has honoured the Islamic and Arab worlds by rejecting the occupation and the US-Zionist project. It has also rejected the so-called governing council, interim government and the elections.
"One of the arrested members of the association has been recently released," al-Qaisi said. "He told us that US forces have set conditions for the release of Shaikh Mahdi al-Sumaidai, saying they will not release him unless he runs in the elections and responds to the US-Zionist project.
Several mosques in Iraq have
been damaged in fighting
"However, Shaikh al-Sumaidai has vehemently denied this," he added.
Shaikh al-Qaisi has linked the attack against the mosque to Shaikh al-Sumaidai's refusal to accept the elections.
"We learnt that Shaikh Mahdi is under pressure and is now in solitary confinement at the airport," al-Qaisi said.
"US forces want a public announcement from him, stating that he accepts the elections. In return, they will financially and emotionally support him," he said. "However, he has remained firm, rejecting the offer entirely."
The mosque is a major landmark in the capital's western district and on the main road leading to Baghdad International Airport.
On 11 November, US-led troops raided the same mosque and arrested the head of the Dawa Association, Shaikh Mahdi al-Sumaidai and about two dozen others.