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As a result of deregulation, distributed generation (DG) systems with distributed generators installed in the middle or low voltage networks become popular in distribution systems. Traditional protections developed in radial systems are difficult in coordination and in protecting against high impedance fault (HIF), sometimes it may cause nuisance tripping in the DG systems. A decentralized multi-agent based protection with capability of HIF detection, fault location and load shedding for the DG systems is proposed in the paper. Digital relay is designed as a relay agent which is capable of searching for information from other relay agents, interacting with other relay agents and performing tasks of protection with autonomy and cooperating. The agent based protection scheme is also presented. EMTP simulation results show that the proposed agent based protection scheme can remove the influence of load switching operations, protect against HIF, electric shock. The prototype of relay agent is developed, the research is now in progress on testing the prototype in dynamic power system.