The fire was sparked by an explosion on an empty fuel barge Wednesday night and spread to a second barge being prepped to be reloaded with natural gas, CNN reported.
At least seven explosions were heard after the fire started.
Three workers were injured and taken to the University of South Alabama Medical Center where they were listed in critical condition, a spokesman said.
Initial attempts to put out the fire were hindered by ongoing explosions.
U.S. Coast Guard Cmdr. Eric King said a 1-mile safety zone was established around the barges and the shipping channel was closed as firefighters allowed the fires to burn.
The incident occurred near the docking area of the Carnival Triumph, King said. The ocean liner has been based at the BAE Shipyard in the Port of Mobile since February when an engine disabled it in the Gulf of Mexico with more than 4,200 people aboard.