At least 16 people have been killed in a raid on a mosque in Baghdad where militants loyal to Shia cleric Moqtada Sadr were based, reports say.
The Mehdi Army controls the area where the clash took place
Aides to Mr Sadr say US forces led the raid on a mosque, while the US says Iraqi troops ran it with US support.
"No mosques were entered or damaged during this operation," the US military said in a statement.
In a second raid, US troops arrested more than 40 Interior Ministry staff said to be guarding a secret prison.
Earlier on Sunday, Iraqi security forces found 30 bodies - many of them beheaded - near the town of Baquba.
In Baghdad, an aide to Mr Sadr accused the US of killing unarmed people at the mosque.
"The American forces went into Mustafa mosque at prayers and killed more than 20 worshippers," Hazim al-Araji told Reuters news agency.
But the US military statement denied that any troops had entered the mosque and said the US special forces troops were on hand only as advisers to the Iraqi troops.
"Iraqi Special Operations Forces conducted a twilight raid in the Aadhamiya neighbourhood in northeast Baghdad to disrupt a terrorist cell responsible for conducting attacks on Iraqi security and Coalition Forces and kidnapping Iraqi civilians in the local area," the statement said.
It said 16 people had been killed. Iraqi police said 22 had died.
AFP news agency said residents close to the scene reported hearing gunfire and ambulances, while black-clad members of Mr Sadr's Mehdi Army could be seen in the streets.
Earlier, in the predominantly Shia city of Najaf, unidentified assailants fired a mortar at the home of Mr Sadr, injuring a child and at least one guard.
There are conflicting reports about the raid on the Interior Ministry building in Baghdad.
A US source said American and Iraqi forces had detained 41 Interior Ministry personnel who had been guarding a secret bunker complex in the building.
But a senior Interior Ministry official denied that ministry staff had been arrested.
AP news agency reported that some 10 Iraqi policemen were held after the 17 prisoners were discovered in the facility.
A deputy interior minister, Major General Ali Ghalib, said the policemen were released when the Americans realised the prisoners were being held legitimately.
Mr Ghalib said the prisoners were of Sudanese origin, and were being held for "violating residency laws".
According to AP, Mr Ghalib said US troops "transferred the Sudanese detainees to another location and they later released the policemen after they had determined that the detention of the Sudanese was legal".
The US military has yet to comment on the reports.
The headless bodies were found at a roadside near Mullah Eid, a village to the south-west of Baquba, Iraqi security officials said.
Sectarian violence between Shias and Sunnis has plagued the area around Baquba since the bombing of a Shia shrine in the city of Samarra in February.
All of those killed were thought to be men. Many had also been shot, officials said.
Also on Sunday, police in Baghdad said they had found at least 13 bodies in various districts of the city, some of which had been handcuffed and shot.
These latest developments come as US Secretary of State Condoleezza Rice suggested that the US could pull significant numbers of troops out of Iraq this year, depending on the security situation.
There are currently about 133,000 US troops in Iraq. The Pentagon is reportedly aiming to cut that number to about 100,000 by the end of 2006.