Nowadays, it is well recognized that flexibility, modularity and reconfigurability are the main challenges in the design of manufacturing systems. Automated warehouse systems play a key role in such systems and are currently controlled using hierarchical and centralized control architectures and conventional automation programming techniques. In this paper, we present preliminary results in developing a flexible, modular and distributed control architecture for automated warehouse systems using Function Blocks and a cyber-physical system perspective. The implementation can be carried on by both IEC 61131 and IEC 61499 standards.