Recently, to improve operating efficiency with the higher in-line rate in automated production lines, a lot of cases of grouping machines and material handling system together to form a cluster has shown frequently. This article addresses the job allocation and operation method of automated material handling for cluster-type production systems. First of all, the control problems of the automated material handling systems are classified into the control problem of inter-cluster material handling system and that of intra-cluster material handling system. Then, a distributed agent-based control scheme is proposed for the former, and an operational control procedure for the latter. Simulation experiment shows that the proposed method is efficient in reducing cycle times and improving utilization of material handling vehicles.