Small motor boats are regularly used in the Suez Canal to 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 US embassy statement said.
"One small boat continued to approach the ship and received two sets of warning shots 20-30 yards in front of the bow."
Egypt's official MENA news agency reported that "an Egyptian citizen was killed and two others injured when a US military vessel opened fire at a small boat."
The embassy said the incident was under investigation and "we express our deepest condolences to the family of the deceased".
Admiral Gary Roughead, chief of US navy operations, said on Tuesday that the leader of the US navy security team had authority to respond.
He said the navy commonly places security detachments on merchant vessels chartered by the US Military Sealift Command to move military cargo.
Sean McCormack, US state department spokesman, said on Tuesday that the US was working with the Egyptian authorities to "make sure that we have good, clear, open communication so you do not have a repeat of these kinds of incidents".