In the age of information proliferation, openness, open information management, interconnectivity, collaboration and communication advances, extended enterprises must be up to date to the new strategic, economic and organizational structures. Consequently, intelligent software based on agent technology emerges to improve system design, and to increase enterprise competitive position as well. The competitiveness is based on the information management, cooperation, collaboration and interconnectivity. Thus, within these interconnectivity and cooperation, conflicts may arise. The automated negotiation plays a key role to look for a common agreement. Argumentation theory has become an important topic in the field of Multi-Agent Systems and especially in the negotiation problem. In this chapter, first, the proposed model MAIS-E2 (Multi-Agent Information System for an Extended Enterprise) is presented. Then an argumentation based negotiation framework: Relationship-Role and Interest Based Negotiation (R2-IBN) framework is presented, and within this framework, the authors focused mainly on, argument generation module via inference rules and argument selection module via fuzzy logic.