This work involves design of an agent based energy auction market mechanism to include storage systems in an interconnected microgrid network using Multi Agent System (MAS) approach. The power system component of a microgrid is modelled using OpenDSS for a standard IEEE distribution network and the communication part is modelled using Java Agent Development Environment (JADE). The communication between JADE and OpenDSS is established through EzJCOM. The markets for both scenarios proposed are cleared initially without considering network losses. In the later part of the paper network losses are quantified and assigned to the appropriate element, and the market prices are revised for DGs, loads and storage systems. The framework is applied on a grid connected microgrid network and validated. It is found that the framework brings harmony between supply and demand of the microgrid thereby reducing the overall market prices.