In manufacturing supply chains with labour-intensive operations and processes, individuals perform various types of manual tasks and quality checks. These operations and processes embrace engagement with various forms of paperwork, regulation obligations and external agreements between multiple stakeholders. Such manual activities can increase human error and near misses, which may ultimately lead to a lack of productivity and performance. In this paper, a multi-agent cyber-physical system (CPS) architecture with radio frequency identification (RFID) technology is presented to assist inter-layer interactions between different manufacturing phases on the shop floor and external interactions with other stakeholders within a supply chain. A dynamic simulation model in the AnyLogic software is developed to implement the CPS-RFID solution by using the agent-based technique. A case study from cryogenic warehousing in cell and gene therapy has been chosen to test the validity of the presented CPS-RFID architecture. The analyses of the simulation results show improvement in efficiency and productivity, in terms of resource time-in-system.