Recently, by increasing penetration of Distributed Generations (DGs) in power systems and its consequence bi-directionality of power flow and variability of fault current, the effect of DGs on conventional protection systems (with fixed setting) become a serious concern. In this study, a communication based decentralized adaptive protection system design is proposed, whereby every protection relay has sufficient intelligence to dynamically calculates and updates its settings based on online identification of prevailing network configurations. Moreover, in the proposed scheme the algorithm of the relay has been further developed to enable relay for proper operation and coordination for post-fault periods. Every relays by obtaining mapping information through real-time communication detects prevailing configuration of the network as well as, once a permanent fault occurs by obtaining fault detection signals detects mapping relationship for post-fault condition an become ready for detection of possible subsequent faults. In order to fast operation, improve reliability and selectivity of the protection scheme, proposed protection system is based on Multi-Agent System (MAS). Different parts of protection system are designed as different agents by their own intelligence, self-tuning and communication abilities.