The raid came despite a truce sealed between Falluja notables and US marines after Thursday's clashes.
Friday's strike hit areas where clashes have been continuing for the past two days between Iraqi resistance fighters and US occupation forces, according to Aljazeera correspondent Abd Al-Adhim Muhammad who witnessed the raid.
"We have received information that US military machinery has entered Falluja and fighting is going on between Iraqi resistance and US occupation forces, but we have not been able to reach those areas," Muhammad said.
A US military plane fired four missiles at a house in the town. Muhammad said the house was owned by a family who left it for a safer place near the town centre.
US occupation authorities announced that they had targeted a safe house used by Abu Musab al-Zarqawi, and killed 20-25 of his men.
Aljazeera's correspondent visited the destroyed house and found four people were injured. Indication of bodies of alleged al-Zarqawi fighters could not be found.
Al-Zarqawi is one of the US' most
Abd al-Adhim Muhammad met the owner of the targeted house and he rejected the claim that his house was an al-Zarqawi hideout.
"Look at the wreckage, is this al-Zarqawi's hideout? Look at the destroyed furniture..." the house owner said.
The strike comes after a ceasefire reached yesterday following the US military's use of 10 laser-guided bombs on targets in Falluja yesterday.
"Whenever we reach a deal with them they break it, and of course the people of Falluja would not keep silent, they have to retaliate," said Falluja notable Abd Allah al-Janabi.
US occupation authorities claim some of the recent air raids have targeted Abu Musab al-Zarqawi and foreign fighters' safe houses in the Iraqi town, west of Baghdad.
Aljazeera correspondent saw
today's US air raid on Falluja
Fallujans have been playing down those allegations with fighters and notables denying al-Zarqawi's presence.
A group of Falluja resistance fighters appeared on TV Friday, reading a statement rejecting US allegations.
"The American invading forces claim that al-Zarqawi, and with him a group of Arab fighters, are in our city," a masked man read from a written statement on Friday.
"We know that this talk about al-Zarqawi and the fighters is a game the American invader forces are playing to strike Islam and Muslims in the steadfast city of mosques."
Al-Janabi addressed a crowd of Fallujans Friday saying al-Zarqawi was being used as a pretext to attack Falluja in the same way unproven WMD allegations were used to attack Iraq.
"Falluja people are brave, bold, and are not afraid from death for the sake of their country. They do not need to have Abu Musab al-Zarqawi among them, they are fully capable of protecting their town and country," al-Janabi said.
Fresh negotiations between Fallujans and US occupation forces to reach a new truce were reportedly under way.