The general hospital's Dr Saleh Hussein said on Friday that most of the victims had been evacuated from the Shuhada district.
US marine spokesman Lieutenant Lyle Gilbert said troops carried out new air raids late on Thursday and opened artillery fire at arms caches in south-eastern parts of the city.
The marines earlier said they were eliminating weapons warehouses in the area, considered a hub for supporters of the Jordanian-born fugitive Abu Musab al-Zarqawi.
"It's artillery you hear ... and AC-130 aircraft are engaging known weapons caches in southern Falluja," Gilbert said.
Witnesses reported thunderous booms shaking the town's southern Shuhada district. Flames lit the sky, while US aircraft droned overhead.
Gilbert said the attacks on the weapons warehouses were triggering secondary explosions.
Earlier, a firefight erupted when Iraqi fighters fired on marine positions with small arms.
"Marines countered these attacks with substantial and proportionate ground fires and air-delivered precision strikes," the marine spokesman said.
Considered a stronghold of al-Zarqawi, Falluja has come under almost daily attacks from US forces.
Determined to regain control of the place, more than 1000 US troops have encircled tit for the past one week.