The raid on Thursday in west Baghdad targeted the homes of Shaikh Harith al-Dhari, secretary-general of the Association of Muslim Scholars (AMS), and Shaikh Abd al-Salam al-Qubaisi, who is in charge of the AMS public relations.
US forces confiscated some items from the two houses but did not harm al-Dhari or al-Qubaisi, sources told Aljazeera.
Muthanna Harith al-Dhari, media spokesman of the AMS, told Aljazeera that the forces entered the house of al-Dhari after they asked the residents to open all doors and send the women to the kitchen.
AMS believes the house searches
were related to events in Falluja
"They threatened residents with dire consequences if any door was left closed, saying their 'dignity' may be harmed," Muthanna al-Dhari said.
"They searched the whole house and fired questions at Shaikh al-Dhari aimed at irritating him."
Muthanna al-Dhari said the forces searched in a similar manner the house of al-Qubaisi, albeit in his absence.
"We believe the searches took place in the context of political pressures accompanying the military assault on Falluja, as the AMS is the main force supporting the city," Muthanna al-Dhari said.
Separately, US-led troops stormed a mosque in Baghdad on Thursday and arrested a preacher who has urged Iraqi forces not to fight alongside Americans attacking the city of Falluja.
"American forces and Iraqi National Guards raided Ibn Taymiya mosque and detained several people, including Shaikh Mahdi al-Sumaydi," said Ala Muhammad, an official with Sumaydi's Higher Committee for Islamic Guidance and Edict.
The US military had no immediate comment.
The US assault on Najaf had been
blasted by Shia clerics now silent
Sumaydi condemned the attack on Falluja earlier this week after a meeting of clerics at Ibn Taymiya mosque. He accused interim Prime Minister Iyad Allawi of waging a war against Iraqis and threatened a "general call to arms".
He also accused top Shia cleric Grand Ayat Allah Ali al-Sistani of complicity in the attack, which began on Monday, through his silence.
Sistani had spoken out against US attacks against Muqtada al-Sadr's fighters in Najaf, but has been conspicuously silent on the sustained US assault on Falluja.