Shaikh Abd al-Hadi al-Darraji, a top aide of the Shia leader Muqtada al-Sadr, told Aljazeera.net that what happened in Masjid al-Rasul (the Prophet mosque) revealed the real intentions of the US occupation forces.
He accused a US soldier of urinating on the Quran and another of consuming alcohol within the chambers of the mosque.
"[This] is a great sin in Islam," al-Darraji said.
"The action of the US forces just days before Sunday's election is a serious provocation and it reveals that the US is serious in insulting the Islamic values and imposing its culture on us.
"They claim they are democratic people, but they are targeting us because we boycotted the elections and said it should not be held under occupation."
Another official in al-Sadr's movement, Naim al-Qaabi, also accused US and Iraqi forces of tearing Qurans during the operation and arresting 21 al-Sadr supporters.
However, neither claims could be immediately verified and the interim Iraqi government issued a statement saying it was investigating the incident.
The US military has not yet commented on the incident.
Al-Sadr led a fierce anti-US uprising last year before toeing the pro-election line, then changed his position again later and vowed to boycott the elections as long as foreign troops remained on Iraqi soil.
Earlier this month, thousands of al-Sadr supporters demonstrated in several cities to protest against petrol and electricity shortages, accusing the interim government of ignoring the people in favour of Sunday's elections.