With robots entering the world of Cyber Physical Systems (CPS), ordering the execution of allocated tasks during run-time becomes crucial. This is so because, in a real world, there can be several physical tasks that use shared resources that need to be executed concurrently. In this paper, we propose a mechanism to solve this issue of ordering task executions within a CPS which inherently handles mutual exclusion. The mechanism caters to a decentralized and distributed CPS comprising nodes such as computers, robots and sensor nodes, and uses mobile software agents that knit through them to aid the execution of the various tasks while also ensuring mutual exclusion of shared resources. The computations, communications and control, are achieved through these mobile agents. Physical execution of the tasks is performed by the robots in an asynchronous and pipelined manner without the use of a clock. The mechanism also features addition and deletion of tasks and insertion and removal of robots facilitating \textit{On-The-Fly Programming}. As an application, a Warehouse Management System as a CPS has been implemented. The paper concludes with the results and discussions on using the mechanism in both emulated and real world environments.