The latest air strike by the US air force was launched on the Shuhada and industrial sectors of the city late on Friday, Aljazeera learned.
Earlier, Ahmad Hardan, member of the Local Council in Falluja, told Aljazeera of the three killed, two were an elderly couple.
Five people were also injured in the air strike which targeted the Dhubbat (officers) neighbourhood in the city, Hardan said.
"Three bodies were taken from the rubble," said one rescue worker. Another three people - among them two women and a child - were injured, ambulance workers said.
A US fighter jet dived over the city's Dhubbat district at around 1730 GMT and shortly afterwards a loud explosion rocked the area, said one resident.
US air raid on Thursday night
killed 44 people in Falluja
An AFP correspondent saw one house damaged in the neighbourhood.
The action follows US air raids on Thursday night near Falluja that killed 44 people, including women and children, according to local hospital officials.
The US military described the earlier raid as a "precision strike" on the compound of suspected al-Qaida member Abu Musab al-Zarqawi.
The attacks came even as Iraq's influential Association of Muslim Scholars (AMS) denounced the air strikes as "terrorist acts".
In a statement to Aljazeera, the AMS pointed out that the victims of the US air strikes were women, children and the elderly.
AMS termed the US assault on
Falluja as "terrorist act"
It urged the international community to earnestly work for an end to the US acts of aggression in Iraq.
Dr Muhammad al-Hamadani, a political analyst, said in an interview with Aljazeera he strongly resented US claims that its air strike near Falluja targeted a site where 90 supporters of al-Zarqawi were meeting at the time.
Al-Hamadani said almost all the victims of the air strikes were women and children, most of them less than 10-years old.
US claim contested
He wondered how these children could be considered followers of al-Zarqawi or that their houses belong to "terrorists" as claimed by the US.
Dr al-Hamadani pointed out that Shaikh Abu Shnatir, whose house was the target, was a prominent and well known tribal leader in the area and it was customary for people to congregate around him and his house especially on a Friday.
"The fact is that the US is pursuing a scorched earth policy that destroys everything on the ground"
Dr Muhammad al-Hamadani,
"The fact is that the US is pursuing a scorched earth policy that destroys everything on the ground. What has happened in Najaf, Falluja, al-Sadr City and Tel Afar is clear proof that this policy has failed," Dr al-Hamadani said.
A cleric in Baghdad, Shaikh Abd Al-Ghafur al-Samarrai, lashed out at the US military for the bombings.
"If you have intelligence on the location of al-Zarqawi and his elements why don't you surround and capture them?" he asked during his weekly sermon on Friday.
US marine killed
A US marine was killed on Friday in Iraq's western province of al-Anbar where Falluja is located, the US military said.
The soldier was killed while conducting what the US military described as "security and stability operations", refusing to give any further details.
On Thursday, three US marines were killed in separate incidents in the province.