Military officials said in a statement on Friday they carried out the attack at 6:33am (0233 GMT) on a courtyard of a house in the southwest part of Falluja.
A hospital in Falluja said it received five injured, including three children, after the bombing.
US military officials said the attack was part of its attempt to strike at suspected hideouts of alleged al-Qaida operative, Abu Musab al-Zarqawi.
"Based on multiple sources of intelligence, the attack targeted 10 to 12 terrorists with known ties to the Abu Musab al-Zarqawi network of foreign terrorists," US Air Force Brigadier General Erv Lessel said in a statement.
But residents in Falluja, exhausted from the US bombing campaign, gave a different version of the events.
"We have nothing to do with the resistance or al-Zarqawi. These are pretexts used by the US military to terrorise the people in Falluja because US soldiers are unable to face the insurgents"
Dr Kamal al-Ani, a doctor at the local hospital, said a US warplane fired a missile that landed in the garden of a house in the Jubail neighbourhood, in southern Falluja. Associated Press Television News footage showed a massive crater beside the house.
"We were sleeping in the morning when a US missile hit our house," Saddam Jasim, the home's owner, said as he and his brother cleared debris.
"We have nothing to do with the resistance or al-Zarqawi. These are pretexts used by the US military to terrorise the people in Falluja because US soldiers are unable to face the insurgents," he said.
"The Americans are lying. Let them come and search us, not hit us with bombs," said an old woman sifting through the wreckage.
"They hit us but we don't know why," she added.
Reuters Television pictures showed bloodstains on the ground in the courtyard.
Resistance fighters in Falluja had
forced US troops to retreat
Over the past month, the US occupying forces have carried out seven attacks against houses in south-western Falluja they claim have been used by Zarqawi or his supporters. About 40 people have been killed in the attacks.
The latest bombing was carried out in coordination with Iraq's interim government, the statement said. Iraq's interim Prime Minister Iyad Allawi is currently out of the country.
US marines retreated from Falluja - a focal point of resistance to the US occupation - after besieging it for three weeks in April. Since then, the US military has been limited to using missiles attacks and bombings to hit the city.
In other developments, a roadside bomb in Samarra killed two US occupation soldiers and wounded another on Thursday.
The US military said the blast killed a soldier on-the-spot while the other died later.
"One soldier died in the attack, and the second died later of wounds from the attack," the US military statement said.
The injured soldier's condition was stated to be stable.
The latest deaths brought to 664 the number of US troops killed in action in Iraq since the start of the US-led invasion in March 2004.
Samarra, 125km north of capital Baghdad, has been the scene of sporadic resistance attacks against the occupation forces.
The fiercest attack was on 8 July when a car bomb explosion killed five US soldiers and four Iraqi guardsmen.