A statement issued by the navy said: "Global Patriot was approached by several boats while preparing to transit the Suez Canal.
"The boats were hailed and warned by a native Arabic speaker on the Global Patriot to advise them to turn away... One small boat continued to approach the ship and received two sets of warning shots 20-30 metres in front of the boat's bow."
The US navy statement said that there were no reports of casualties and that all shots fired were accounted for.
However, Egyptian security officials said Mohammed Fouad Afifi Gaafer, an Egyptian trader, was killed by bullets fired by the Global Patriot and was buried after local authorities turned the body over to his family.
The US ship had been waiting to pass through the Suez Canal from the Red Sea to the Mediterranean.
Egyptian officials said that the ship continued its journey through the canal and was expected to arrive at Port Said near the Mediterranean by nightfall.
The US navy contracted the ship in February to carry military goods to locations including some in the Gulf, Reuters news agency reported, citing a military spokesman.
The Suez Canal is an important source of foreign currency for Egypt, and about 7.5 per cent of world sea trade passes through it.