American media reported at least seven casualties.
North Carolina Governor Roy Cooper has urged residents in the path of the storm to "stay in a sheltered place" as Florence will "continue its violent grind across the state for days".
Firefighters in North Carolina took a moment to kneel and pray at the site where a mother and baby were killed by a tree that fell down during Hurricane Florence.
The third death happened in Hampstead, Pender County when a woman had a medical emergency and EMS crews could not get to her due to the storm, according to Tom Collins, Director of Emergency Management.
Horry County officials told The Sun News that emergency personnel are still responding to calls and never stopped. A 78-year-old man was electrocuted attempting to connect extension cords while another man perished when he was blown down by high winds while checking on his hunting dogs, a county spokesman said.
Storm surges - the bulge of ocean water pushed ashore by the hurricane - were as high as 10 feet (3 meters).
"Our house is on high ground so we're not anxious about the flooding", he said.
He said "24 to 36 hours remain for significant threats" from heavy rain, storm surge and flooding. My wifes in a panic right now.
Dan Eudy said he and his brother were awakened on Thursday night by the sound of a boat ramming against his front porch. Areas from Wilmington through Fayetteville to Charlotte will experience 500-year to 1,000-year flood events, he said.
It's since slowed down even more than it had been - moving west at just 2 miles per hour.
By Friday night the center of the storm had moved to eastern SC, about 15 miles northeast of Myrtle Beach, with maximum sustained winds of 70 mph.
The homes of about 10 million were under watches or warnings for the hurricane or tropical storm conditions.
More than 20,000 people are staying in 157 emergency shelters in North Carolina, Cooper said.
The centre of the hurricane's eye came ashore close to Wilmington, with sustained winds of 150km/h the National Hurricane Center (NHC) said.
Some towns have already had over 60 centimetres of rain and forecasters warn that totals could hit one metre.
On Friday, coastal streets in the Carolinas flowed with frothy ocean water, pieces of torn-apart buildings flew through the air, and at least 525,000 homes and businesses were without power, almost all of them in North Carolina.
The White House said President Trump will tour areas affected by Florence next week, once it is determined that his visit will not disrupt rescue and recovery operations.