A system and method for automated handling, transferring and storing conventional cargo storage containers on a cargo ship wherein the containers are stored in a multi-tier cell system and are manipulated by powered transfer units which are selectively moveable along an intersecting overhead track system such that containers may be simultaneously retrieved from, moved or placed within any of the cells of the ship. The transfer units are equipped both with hoists, which control spreader beams which are selectively secured to the cargo containers, and guide stabilizers, which prevent undesirable movement of the cargo containers when they are elevated above the cell structures such that the containers may be manipulated even during rough sea conditions such that the system is essentially continuously operable as a floating supply distribution system.