A senior US defence official put militant losses at more than 500.
There was no word on civilian casualties amid the strict curfew in force in the city.
Despite initial successes and superior firepower, fierce fighting exploded in the Jolan district of north-western Fallujah, where the heart of the resistance is thought to beat.
Fires blazed across the battle-torn neighbourhood as night fell, while the US military pounded targets with heavy shelling, an AFP photographer said.
"We control about 75 percent of the city. The more we go in the more we find the fight is becoming fiercer," said marine Major PJ Batty.
Some areas fell easily, but die-hard fighters refused to back down in Jolan where persistent firefights lit up the night sky.
A day after the Iraqi military said it had found a "slaughterhouse" in Fallujah where foreign hostages had been executed, Batty said three Iraqi hostages were found in "basements, handcuffed by their hands and ankles, starving, thirsty and tortured."
He said the military was on course to retake the city by Saturday morning.
In the face of the relentless onslaught in Fallujah, insurgents shifted their focus elsewhere, with a spate of bombings and other attacks across central and northern Iraq, that have prompted the authorities to impose curfews in seven cities.
At least nine people were killed, many burnt to death in their cars, and 25 wounded when the car bomb exploded in Baghdad, police and medics said.
Flames raged around one car with four children trapped inside after the blast ripped through a line of vehicles at the peak of the morning rush hour.
Two US helicopters were forced to make an emergency landing after taking small arms and rocket-propelled grenade fire, a military spokeswoman said, adding that there were no casualties.
In Mosul, a US military spokeswoman said several militants were killed in ground and air attacks launched at the request of the provincial governor. In Ramadi, medics said three people were killed, including a policeman and an attacker, and 17 wounded during skirmishes between insurgents and US troops.
In Hawija a night time curfew was imposed after a mortar attack on a national guard compound wounded eight people, half of them Iraqi national guards, the local police chief said.
And in the city of Samarra, which was retaken from insurgents in a major offensive last month, four people were killed and eight wounded in fresh violence, local officials said.