The paper solves the problem of controlling the handling of container ships in a tandem seaport. The control system for container ships includes determining the route of ships taking into account random disturbances, ship transport time and the time of unloading/loading. Determining the optimal route of ships is an NP problem. The ship service process is scheduled on a weekly basis. However, the tugboats operate in a shift cycle. It is important to designate a warehouse/wharf where containers are to be unloaded/loaded and to determine restrictions. The port consists of a roadway, ships, unloading and loading quays, canals, and warehouses and can have various structures. It is assumed that the ships await service in the port roadstead. The time horizon for the allocation is one week. Ships waiting in the roadstead have priorities depending on the waiting time. It is assumed that the time of transport, unloading/loading of the vessel and economic parameters are given. The optimization of ship service in the port is multi-criteria. There are entry, exit and internal criteria. The problem of controlling container ships in a tandem seaport was solved by the method of artificial intelligence using a computer program. The optimization criterion was the minimization of vessel service time in both parts of the port, taking into account restrictions. A logistics system for controlling ships in a tandem seaport with averaged data and random events was developed.