A mother and baby were killed when a tree fell on a house, according to a tweet from Wilmington police. The child's father was transported to the hospital with injuries.
Nearly 800,000 people are reported to be without power already in North Carolina, and officials have warned restoring electricity could take days or even weeks.
The hurricane has moved at only 3-6 miles per hour on Friday, increasing the effect of its torrential rains.
The extremely unsafe hurricane has already caused more than 500,000 power outages and more is expected in the coming days.
More than 60 people had to be pulled from a collapsing motel at the height of the storm, and many more who defied evacuation orders held out hope of being rescued.
"WE ARE COMING TO GET YOU", the city of New Bern tweeted around 2am local time. "You may need to move up to the second story, or to your attic, but WE ARE COMING TO GET YOU", the New Bern authorities said on Twitter. The slow-moving storm is expected to dump as much as a metre of rain and bring a storm surge of up to three metres in some areas.
Florence was moving west south-west at about 5 miles per hour (7 km/h), with its center located over eastern SC.
The city of 29,000 that's near the North Carolina coast is surrounded by two rivers on the east and south. The remnants of Florence are expected to hit the peaks of western North Carolina in a couple of days. "It's an uninvited brute who doesn't want to leave".
"This storm is going to continue its violent grind across our state for days", North Carolina Governor Roy Cooper said. He said parts of North Carolina had seen storm surges - the bulge of seawater pushed ashore by the hurricane - as high as 10 feet.
The storm is expected to track across SC over the weekend.
Authorities warned too of the threat of mudslides and the risk of environmental havoc from floodwaters washing over industrial waste sites and pig farms.
Florence was inching along Friday night, trapping people in flooded homes and promising days of destruction and human suffering. At 5:30 a.m. a reporter in a downtown hotel here in Wilmington heard the signature hurricane sound - a low, heavy humming combined with an nearly musical high note. The man's family found his body Friday morning at his home, Dail said. Hurricane-force winds extended 80 miles (130 kilometres) from its centre, and tropical-storm-force winds reached out 195 miles (315 kilometres).
In Jacksonville, North Carolina, city officials posted photos of toppled gas pumps and a downed trees early Friday, warning residents to take shelter and avoid roadways.
Griffin said she was jolted awake when the power went off at the hotel as some of the storm's strongest bands lashed Wilmington with wind and rain.
And about 46 miles farther up the waterfront, in New Bern, two FEMA teams were working on swift-water rescues and more were on the way. In South and North Carolina evacuated residents of coastal areas is just over 1.5 million people. She died Friday morning.
Duke said it had more than 20,000 personnel ready to start fixing outages as soon as conditions allowed, including over 8,000 from Duke's Carolinas utilities, 1,700 from the Midwest, 1,200 from Florida and 9,400 from other utilities.
The organization is sending truckloads of relief supplies that it says will reach over 10,000 of the most vulnerable people impacted by the storm.