This paper deals with the multi-agent manufacturing system with application of bio-inspired techniques and new approaches to the development trends of advanced industrial engineering (AIE) in energy efficient manufacturing. This integration represents a sustainable development so that more effective use of natural and energy resources is achieved and energy costs are reduced. The new solution of reference model for control and coordination decentralized systems - CODESA is proposed. Centralized architecture suffers from various problems, such as rigidity, scalability, low fault-tolerance or very limited ability for flexibility, agility and productivity. Prime is concrete application of CODESA in manufacturing domain. Its concrete application, CODESA-Prime, was verified in simulation logistics multi-agent system.