It 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.
Officials said in a statement Wednesday that crews are using the "utmost safety" in cleaning the spill of pentaerythritol tetranitrate. The port was expected to open at 8 a.m. Officials didn't say when the port would open.
The cleanup is being performed under the direction of the U.S. Coast Guard.
No reported injuries or environmental damage has been reported at the facility.
"The Ports Authority's goal is to reopen the Port of Morehead City as safely and as quickly as possible," said CEO Thomas J. Eagar.
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."
Following the incident, Gov. Bev Perdue released a statement: "I want to commend the local, state, and federal officials who have worked diligently today responding to the hazmat incident at the Morehead City Port," she said. "Work is progressing well on containing the materials, and the clean-up will follow soon afterwards. Our top priority is protecting public safety, and I urge citizens to follow the advice of Carteret County and other emergency personnel on the scene."