The Navy said it believes the fire began somewhere in a lower cargo hold where marine equipment and vehicles are stored, and that an explosion was probably caused by a change in air pressure.
Sobeck told the San Diego Union-Tribune there were no weapons or munitions on board.
The ship’s million-gallon fuel tanks were also situated “well below” the fire and were not the source of the blaze, said Sobeck.
The fire is likely being fueled by paper, cloth, rags or other materials, Sobeck said.
Only 160 crew and officers were on board when the explosion happened. Routinely a thousand sailors could be on the ship when on active duty, said Mike Raney, a spokesman for Naval Surface Force, U.S. Pacific Fleet.
Sobeck said Sunday that 17 sailors and four others, including firefighters, were initially hospitalized with non-life-threatening injuries.
The blaze is said to be burning deep within the interior of the ship, but flames have also been seen above deck.
The USS Fitzgerald and USS Russell, which were docked nearby, have been moved.
The blaze has proved stubborn, requiring helicopters to drop water from above, firefighting vessels to shoot water from the bay, and fire trucks to direct water hoses from the dock, according to The Associated Press.
“We are grateful for the quick and immediate response of local, base, and shipboard firefighters aboard USS Bonhomme Richard,” Gilday said in a statement.
The 23-year-old ship has the capacity to deploy and land helicopters, smaller boats and amphibious vehicles. Because of its age, a fire could be particularly destructive, especially if it reached the engine room and other tight spaces with machinery, said Lawrence B. Brennan, a professor of admiralty and international maritime law at Fordham University in New York.
“The heat of a fire of this nature can warp the steel, and that can be a major problem for any ship,” said Brennan. “On an older ship, it’s even more of a problem.”
— Information provided by The Associated Press was used to supplement this report.