The ship had been wandering into Egypt’s territorial waters after departing from the Occupied Palestinian Territories, according to Egyptian media.
The seizure took place on Thursday after the vessel, which was heading from the Israeli port of Eilat to Togo, strayed into Egyptian waters, the reports said.
The vessel was carrying 105 crates of unspecified weapons and ammunition as well as a crew of 14, who were detained by Egypt's navy.
Security officials had said the vessel would be held while authorities investigate whether it was carrying smuggled weapons.