This research aims to propose a multi-agent based hierarchical model for the operations of container terminals. We have divided our model into four key agents that are involved in each sub processes. The proposed agent allocation policies are recommended for different situations that may occur at a container terminal. A software prototype is developed which implements the hierarchical model. This web based application is used in order to simulate the various processes involved in the following operations on the marine side in a case study of a container terminal in Sweden by adopting a multi-agent based simulation technique. Due to the increase in usage of container transportation, container terminals are experiencing difficulties in the management of the operations. The software provides a decision support capability to terminal managers for scheduling and managing the operations effectively while also visually presenting the time it takes to complete the process and its associated cost. Terminal managers need to implement certain policies to improve the management and operations of the container terminal. The policies are evaluated and tested under various cases.