In the immediate aftermath of the incident late Monday, the U.S. Embassy in Cairo and the U.S. Navy maintained that according to the security team aboard the vessel there were no casualties.
But on Wednesday, an embassy statement said it "appears that an Egyptian in the boat was killed by one of the warning shots."
Mohammed Fouad was buried Tuesday amid expressions of anger against the Egyptian government and the U.S. by family members.
"We express our deepest sympathies to the family of the deceased," Vice Adm. Kevin J. Cosgriff, Commander, U.S. 5th Fleet said in a statement. "We are greatly saddened by events that apparently resulted in this accidental death. This situation is tragic, and we will do our utmost to help take care of the family of the deceased."
Cosgriff added that the investigation was continuing to determine exactly what happened.
"We're concerned about doing the right thing and helping to take care of the family," 5th Fleet spokeswoman Cmdr Lydia Robertson told The Associated Press.
The Navy has been leery of small boats getting near its warships since al Qaeda suicide attackers rammed an explosives-packed motorboat into the USS Cole off Yemen, killing 17 sailors in 2000. Cmdr. Lydia Robertson, spokeswoman for the Bahrain-based U.S. 5th Fleet, said cargo ships sailing under contract to the Navy follow the same rules of engagement as American warships in dealing with approaching boats.
The Global Patriot, a civilian ship under short-term contract to the Navy, was approached by small motor boats that often conduct informal commerce with canal shipping.
"The boats were hailed and warned by a native Arabic speaker using a bullhorn to warn them to turn away. A warning flare was then fired," the embassy said Tuesday. "One small boat continued to approach the ship and received two sets of warning shots 20-30 yards in front of the bow."