The scheduling problem of large products like ships, airplanes, space shuttles, assembled constructions, and automobiles is very complex in nature. To reduce inherent computational complexity, we often design scheduling systems that the original problem is decomposed into small sub-problems, which are scheduled independently and integrated into the original one. Moreover, the steep growth of communication technology and logistics makes it possible to produce a lot of multi-nation corporation by which products are produced across more than one plant. Therefore vertical and lateral coordination among decomposed scheduling systems is necessary. In this research, we suggest an agent-based coordinating mechanism for multi-level scheduling systems in supply chain. For design of a general coordination mechanism, at first, we propose a grammar to define individual scheduling agents which are responsible to their own plants, and a meta-level coordination agent which is engaged to supervise individual scheduling agents. Second, we suggest scheduling agent communication protocols for each scheduling agent topology which is classified according to the system architecture, existence of coordinator, and direction of coordination. We also suggest a scheduling agent communication language which consists of three layers : Agent Communication Layer, Scheduling Coordination Layer, Industry-specific Layer. Finally, in order to improve the efficiency of communication among scheduling agents we suggest a rough capacity coordination model which supports to monitor participating agents and analyze the status of them. With this coordination mechanism, we can easily model coordination processes of multiple scheduling systems. In the future, we will apply this mechanism to shipbuilding domain and develop a prototype system which consists of a dock-scheduling agent, four assembly-plant-scheduling agents, and a meta-level coordination agent. A series of experiment using the real-world data will be performed to examine this mechanism.