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Wireless Sensor Network (WSN) is an indispensable component of pervasive computing. Mobile agents are used for several applications in WSNs such as data fusion, localization, re-allocate, and update of tasks on sensor nodes, etc. Middleware can provide a platform to these different applications to work concurrently and independently on top of sensor node's operating system. WSN often suffer from low availability of resources. Thus they cannot afford to implement effective security mechanisms at application or hardware layer. In this article, we propose a middleware architecture for mobile agent based WSN applications that is not only efficient for traditional tasks, but also capable of providing adequate security services. As a case study, we explore mobile agent based intrusion detection system, considering as an application, for our proposed middleware architecture. Comparative study and detailed analysis of proposed middleware architecture show a number of benefits.