Canal authority head Mohab Mamish said a "terrorist element" targeted a Panama-flagged vessel yesterday, but it was undamaged.
There were reports of two blasts, but details of the attack are unclear, BBC reported.
Egypt's Sinai has been hit by a wave of violence since Islamist President Mohammed Morsi was ousted from power by the army on July 3.
The reports said there were two explosions late last night as the ship, Cosco Asia, passed through the waterway.
The Suez Canal, between Port Said and Suez, is one of the most important waterways in the world. It is a vital global trade route between the Red Sea and Mediterranean.
The canal is extensively used by modern ships , as it is the fastest crossing from the Atlantic Ocean to the Indian Ocean. Tolls paid by the vessels represent an important source of income for the Egyptian government.
It is unknown whether the attack was linked to the continuing protests by Muslim Brotherhood supporters against the ousting of President Morsi.
The unrest has spilled over into the Sinai peninsula, where Islamist militants have carried out frequent attacks on the authorities.
Al-qaeda is suspected of being behind the attack.
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