He said parts of the state had seen storm surges - the bulge of seawater pushed ashore by the hurricane - as high as 10 feet.
Two people died in Wilmington after a tree fell on their house, the city's police department said.
The child's father was transported to a hospital with injuries, according to Wilmington police.
Antonio Ramirez, a construction worker from El Salvador living in Leland, North Carolina, said he planned to ride out the worst of the weather with his dog Canelo.
A third person, a woman, died in Hampstead, NC, in Pender County.
The town of Oriental, North Carolina, had gotten more than 18 inches of rain just a few hours into the deluge, while Surf City had 14 inches and it was still coming down.
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Florence was seen as a major test for the Federal Emergency Management Agency, which was heavily criticized as slow and unprepared previous year for Hurricane Maria in Puerto Rico, where the storm was blamed for almost 3,000 deaths in the desperate aftermath.
Speaking during a visit to Moscow less than an hour after the hurricane made landfall in North Carolina, Perry said "we've done this many times before". That number was down to 40 later in the day.
Emergency declarations were in force in Georgia, South and North Carolina, Virginia, Maryland and the District of Columbia. "You're going to have flooding miles and miles inland", the center's director, Ken Graham, said. "Plant procedures call for the reactors to be shut down before the anticipated onset of hurricane-force winds", agency spokesman Joey Ledford told CNN.
Satellite image taken on 14 September, 2018, shows Hurricane Florence hitting the U.S. east coast. "Our meteorologists are saying that the rainfall amounts will be devastating in certain areas", he said Thursday.
One of the rescuers in New Bern was Jason Weinmann, a retired Marine who has a military troop transport vehicle he bought at a government auction.
He added that 20,000 people were being housed in shelters across the state.
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"It was pretty bad. So we made a decision to stay", she said.
The Neuse River in New Bern, North Carolina yesterday began to flow over its banks, triggering flooding as waters continued to rise from torrential rainfall. "We are stuck in the attic".
Besides federal and state emergency crews, they were being helped by volunteers from the so-called "Cajun Navy" who also turned up in Houston during Hurricane Harvey to carry out water rescues.
New Bern resident George Zaytoun chose not to evacuate and is trapped inside his home. It shows the depth of water in a Belhaven family's garage.
More than 60 people had to be pulled from a collapsing cinderblock motel at the height of the storm. According to the South Carolina Department of Public Safety, a pick-up truck drove into standing water on the road and lost control, overturning into a ditch.
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With destructive winds and blinding rains ripping off the tin roof of a building and toppling over this gas station. Though it will weaken from a super typhoon to a severe typhoon, it will still be packing sustained winds of 109mph.