Antiquities Minister Mohammed Ibrahim said in a statement on Friday that officials found the artefacts while searching cargo on Thursday at the coastal city of Damietta.
Among the artefacts are a cylindrical wooden box plated in silver, which would have held Torah scrolls. Officials also found a silver knife dating to roughly 1890 with inscriptions, and bells commonly hung in synagogues.
A committee will study and date the cache, which the statement says "embodies a period of religious tolerance in Egypt's history".
Egypt has experienced a security vacuum since its 2011 uprising. Thousands of artefacts have been stolen.