The skull was discovered during a dredging operation in April under 40 feet of water, U.S. Navy officials said.
Scientists with the military's Joint Prisoners of War, Missing in Action Accounting Command were conducting a forensic analysis of the skull to determine whether it belonged to a Japanese pilot, said Don Rochon, spokesman for the Naval Facilities Engineering Command Pacific in Hawaii.
It was found intact, along with forks, metal scraps and a soda bottle from the 1940s, said Denise Emsley, spokeswoman for the Naval Facilities Engineering Command in Hawaii.
But she cautioned that the skull may not come from a Japanese fighter pilot.
"Hawaii has a very large Asian population now and it had a large Asian population in the 1940s," Emsley said. "It could have been from someone who worked on the piers."
About 2,400 lives were lost due to Japan's December 7, 1941, surprise attack on the U.S. Naval Base at Pearl Harbor, and another 1,178 people were wounded.