The fighters threw grenades at the marines, Lieutenant General John Sattler said on Friday. Three fighters were also killed in the incident which took place on Thursday.
Marines have been searching houses in Falluja for weapons and fighters after a major offensive in the town earlier this month.
While the US military said they had killed more than 1000 fighters in the offensive, the marines still face resistance in Falluja, where many buildings were reduced to piles of rubble.
"We will keep searching for weapons until we put a 'green X' on the last house in Falluja," Sattler said.
Marine officers have said they would inspect an estimated 50,000 houses in the city west of Baghdad, a tedious task that involves searching everything from ventilation systems to couches as snipers await opportunities to fire.
Meanwhile, fighters in Falluja have claimed in a statement that they had reorganised and resumed their attacks.
"After reorganising, the Mujahidin resumed their attacks on Wednesday with the aim of shattering the myth of the invincibility of the coalition forces, and the traitors and collaborators who are under the orders of Allawi and Naqib," they said.
Falluja's fighters say they have
now reorganised themselves
The statement issued on Friday by the Mujahidin Council was referring to interim Iraqi Prime Minister Iyad Allawi and Interior Minister Falah Naqib, both staunch supporters of the vast operation launched on 8 November.
Clash in Kirkuk
In a separate development, armed fighters attacked a police station near the northern city of Kirkuk, killing one policeman and injuring three, police said on Friday.
Fighters used machine guns and rocket-propelled grenades in their assault on a police station in Rashad, 50km southwest of Kirkuk on Thursday night, according to police Brigadier Sarhat Qadir.
Qadir said policemen returned fire, forcing the attackers to flee the scene. Kirkuk is 290km north of Baghdad.
Death in Samarra
Meanwhile, in Samarra, which was recently occupied by US forces after remaining a no-go zone for months, a political activist has been gunned down by unknown attackers.
Reoccupation of Samarra has
failed to put an end to violence
"Nabil Said Darwish, a member of the National Salvation Movement, was assassinated this morning by armed men in Samarra," police Lieutenant-Colonel Mahmud Muhammad said on Friday.
The party is led by Wafiq al-Samarrai, a former general under Saddam Hussein who broke away from the regime shortly before the US-led invasion of Iraq in March 2003.
"Darwish had survived several assassination attempts over the past two months, which had left two of his bodyguards dead," the police officer said.
Fighters in Samarra, 128km north of Baghdad, accuse the party of having links to the US military.