Integrating physical objects with the corresponding enterprise applications any time any where is the essential issue for a real-time enterprise. This study proposes a multi-agent system framework called agent-based manufacturing control and coordination (AMCC) system, a agent-based framework using ontology and RFID technology to monitor and control dynamic production flows and also to improve the traceability and visibility of mass customization manufacturing processes. The capabilities offered by multi-agent systems to respond to RFID events in real-time and a broad class of agent design and coordination issue regarding just in time (JIT) and just in sequence (JIS) manufacturing processes are also exploited in this study. To validate the proposed framework, case study of a bicycle manufacturing company is used to demonstrate how the proposed framework can benefit its JIT production. Finally, an example prototype system is implemented to demonstrate the concept of the proposed framework.