The US military released a statement confirming the raid on Tuesday saying troops came under fire while entering the building in the village of Adwar, and that soldiers shot dead two men inside.
A woman was killed and one child was injured, but it was unclear who shot them, the statement said.
Lieutenant Michael Street, a US military spokesman, said: "During an intelligence-driven operation near Tikrit this morning, coalition forces came under small-arms fire as they entered a building.
Iraqi police, relatives and neighbours said a couple and their 19-year-old son were shot to death in their beds late Monday.
Police said two young girls were wounded and one died on Tuesday at a hospital.
It was the second time in as many days that the US military conceded involvement in the death of Iraqi civilians.
Suicide attack
On Monday, the military said it had accidentally killed nine Iraqi civilians, including a child, in an air raid late on Saturday targeting al-Qaeda in Iraq south of Baghdad.
Elsewhere a suicide bomber killed at least eight members of a group opposed to al-Qaeda at a checkpoint outside a Sunni tribal sheikh's house in central Iraq, police said.
The attack took place outside the home of Sheikh Shathr al-Obeidi, head of a tribal "Awakening" group on Tuesday, in Awad village near Taji, 40 km north of Baghdad, he said.
"Eight members of the Awakening were killed at the checkpoint. Several were wounded," the officer said on condition of anonymity.
"Awakening groups" have confronted al-Qaeda in Iraq with the support of the US military for more than a year.
US commanders have said that al-Qaeda have been increasingly forced to resort to suicide attacks because their ability to stage major bombings has been reduced.
Tuesday's attack follows a spate of suicide bombings in Iraq that have killed more than 200 people already this year.
The attacks have mostly taken place in the province of Diyala province which is now considered Iraq's most dangerous region.