The incident happened just before 5 a.m. Tuesday when a forklift punched through the side of a large container puncturing five barrels inside.
There were no injuries and the problem was contained to land, nothing was in the water.
The port was expected to open at 8 a.m Wednesday, but it took crews longer than expected to clean the area.
It was re-opened Thursday afternoon.
Authorities in Morehead City lifted a voluntary evacuation order late Tuesday evening.
According to Morehead City Fire Chief Wes Lail, the chemical involved is Pentaerythritol tetranitrate (PETN), which is one of the most powerful high explosives known.
It's the same material that 23-year-old Nigerian Umar Farouk Abdulmutallab allegedly tried to use to bring down a Northwest flight approaching Detroit on Christmas day.
Highway 70 had to be closed from 4th Street in Morehead City to the Morehead-Beaufort high rise bridge.
Business owners were not happy that no foot or vehicle traffic was permitted in the port area Tuesday.
"It's a setback for the business, but it's also a setback for the employees," restaurant owner John Poag said. "I mean, they're losing a day's wage here as is everybody in downtown Morehead City."
The accident is also a big loss for the state, but it'll take a while to figure out the cost of shutting down the port.
Port police said they knew the shipment of PETN was coming and they had extra security in place, but they won't say who ordered it or where it came from.
Morehead City is one of the deepest ports on the East Coast - dealing in large amounts of sulfur products, phosphate and rubber. Last year, it exported more than 2,000 tons of material classified as "military."