Iraqi Prime Minister Ibrahim al-Jaafari has expressed concern to US military authorities about a clash near a mosque in a Shia area of Baghdad on Sunday.
Accounts of the raid, in which about 20 people were killed, remain confused with disagreement about the role of US forces and the identity of the dead.
US officials say Iraqi special forces led the raid, backed by US advisors, to disrupt an armed insurgents' cell.
Angry local residents say many of the dead were unarmed Muslim worshippers.
A spokesperson for Mr Jaafari said he was "deeply concerned" and had telephoned US military commander General George Casey, who had promised a full inquiry.
Relatives have begun burying the bodies in funerals marked by anger and bitterness.
"No one is protecting us," shouted one distraught mourner, Hamid Taayab, who said only radical cleric Moqtada Sadr's Mehdi Army militia prevented Iraqis "being slaughtered in our homes".
Iraqi television has been showing footage of bloody corpses at what was said to be Sadr City's Mustafa mosque.
Many of the dead were elderly and their identity papers indicated they were members of prominent political parties, according to the TV footage.
The US military said the bloodshed happened after Iraqi commandos and soldiers from the Iraqi counter-terrorism force came under fire during a house-to-house search for insurgents.
Members of the US special forces were said to be present "in an advisory capacity". The fighting took place in an office adjacent to the mosque, and the US military insisted no religious site was entered or damaged.
Initial reports had characterised the violence as a clash between forces loyal to Mr Sadr's and US forces, and then as a massacre inside the Mustafa mosque.
Large numbers of weapons were found, the US military said, and an abducted employee of the ministry of health was freed, after a 12-hour ordeal of beating.
A senior supporter of Mr Sadr rejected the US account, saying: "This is a lie, we saw unarmed worshippers and we didn't find any Iraqi weapons. This place was just for praying and worshipping."
Separately, police say nine more bodies with signs of torture and strangulation have been discovered in Baghdad.
The bodies were discovered dumped in empty ground used to sell used cars in the west of the city.
Three other bodies, two male and one female, were found shot in the head in east Baghdad late on Sunday, police said.
Earlier the bodies of 30 men, most of them decapitated, had been found in Baqouba north-east of the capital.
Only 18 of the bodies were reported to have been recovered after the grim find at dusk on Sunday in Mullah Eid village.
Reports say that initial recovery operations were difficult in the gathering darkness and the insecure conditions prevailing in that part of Diyala province.
Scores of corpses have been turning up daily in and around Baghdad in a wave of sectarian killing since the destruction of an important Shia shrine in Samarra on 22 February.