Adnan al-Dulaimi, secretary-general of the Conference for Iraq's People, said soldiers in tanks and Humvees, with two helicopters circling overhead, broke into his home at 2.30am (local time) on Thursday, put his family and himself in a guest room and searched the house.
"It was as if they were attacking a castle, not the home of a normal person who advises Iraq's interim government and has called for reconciliation and renounced sectarianism," al-Dulaimi told a news conference after the raid in western Baghdad.
Al-Dulaimi, who is a prominent critic of the Shia-led government, said the troops arrested four of his bodyguards and confiscated their licensed weapons.
He said the Americans were acting on false tips that linked the men to anti-government fighters.
"This act of humiliation ... derails our efforts to encourage Sunnis to take part in the political process," said al-Dulaimi, urging the US government to stop such actions.
The other raid took place at the Baghdad home of Harith al-Obeidi, another senior official in the organisation, said Iraq's largest Sunni political party, the Iraqi Islamic Party.
The US military said it had conducted several raids in those areas of Baghdad on Thursday, but could not immediately identify the homes or Iraqis involved.
The chief of Iraqi police in the district, Major Moussa Abdul-Karim, said he heard reports of the raids after they took place but the US military had not coordinated with the Iraqis.
"This act of humiliation ... derails our efforts to encourage Sunnis to take part in the political process"
Conference for Iraq's People
The Conference for Iraq's People and the Iraqi Islamic Party are two leading political organisations representing Iraq's Sunni Arab minority, which has increasingly complained of abuse as US and Iraqi forces pursue anti-government fighters, the bulk of whom are Sunnis.
The two groups are also campaigning to defeat a draft constitution in 15 October referendum, believing it will divide Iraq into Kurdish, Shia and Sunni areas, with the Sunni one having the least power and revenue.
The Iraqi Islamic Party condemned the two raids as "a savage act" and an "unjustifiable aggression", saying such treatment of "good Iraqis" could set back efforts to persuade citizens to join efforts to improve security in the war-torn country.