The economical property of a shipping enterprise, as well as other transportation industries, is determined by the difference between the freight earned and expense paid. This study can be regarded as a division of optimizing ship allocation to routes under the integrated port transport system. Fleet planning and scheduling require complicated allocations of cargoes to ships and ships to routes in order to optimize the given criterion function for a given forecast period. This paper deals with the optimum ship allocation problem minimizing the operating cost of ships in a shipping company. Optimum fleet operating for a shipping enterprise is very important, since the marine transportation is a form of large quantity transport requiring long-term period, and there is a strong possibility to bring about large amount of loss in operation resulting from a faulty ship allocation. Where there are more than one loading and discharging ports, and a variety of ship's ability in speed, capacity, operating cost etc., and when the amount of commodities to be transported between the ports has been determined, then the ship's schedule minimizing the operating cost while satisfying the transport demand within the predetermined period will be made up. First of all a formula of ship allocation problems will be established and then will be constructed to solve an example by the Integer Programming application after consideration of the ship's ability, supply and demand of commodity, amount of commodity to be transported, operating costs of each ship etc. This study will give good information on deciding intention for a ship oprator or owner to meet the computerization current with shiping management.