The paper describes the design of mission planning and control architecture for an autonomous material handling system which perceives the live requirements of material movement on a factory floor and does judicious deployment of autonomous guided vehicles (AGVs) to service them. The system has a novel methodology to perceive prevailing situation on factory floor in terms of material transportation and fetching suitable mission, from a predefined set, for execution. This research effort is part of a long-term project that aims to enable AGV to carry out loading and delivery missions in hazardous areas of fuel fabrication facility, in a completely autonomous mode. The system is being used as an advanced test bed to test developments in mission planning and real-time mission execution system for AGVs. The system consists of single or multiple AGVs transporting material between several loading and delivery points, through a structured environment. It modularizes all aspects of factory automation like floor configuration, individual vehicle control, mission execution, high-level mission planning, and coordination. We present a methodology of building complex missions in terms of unique operations. In the later part, we present a case study based on a real scenario for evaluating the performance of indigenously developed AGV in simulation.