Two Iraqi security troops were also killed.
US forces fired heavy artillery at some houses in the south-eastern neighbourhood of Shuhada, leaving two dead and six wounded, said Dr Raid Muhammad of Falluja General Hospital.
Four of the wounded were listed in serious condition, Muhammad added.
Later, a second official, Dr Nabil Khuri, identified the two Iraqi soldiers and said the area hit was an Iraqi army camp bordering a residential neighbourhood.
The US military had no immediate confirmation of the attack.
Falluja is said to be at the centre of Sunni Muslim resistance to the US invasion and US-led forces in Iraq.
A US air strike in a residential area of the city killed 20 people on Wednesday.
The US military has been using heavy artillery and aerial assaults on alleged resistance positions in Falluja since the city became a no-go zone for US troops after an April offensive ended with an agreement for Iraqis to police the area themselves.
In an interview with Aljazeera, General Lance Smith, Deputy Commander of the US central command centre, said US forces only attacked a house which was under surveillance for a while.
"The situation in Fallujah, and other cities, is under (US appointed) Prime Minister Iyad Allawi's control and whatever the (US appointed) interim Iraqi government decides, we would support but they have to decide if the situation warrants political or military solutions", Gen Smith added.