Logistics systems provide their service to customers by coordinating the resources with limited capacity throughout the underlying processes involved to each other. To maintain the high level of service under such complicated condition, it is essential to carry out the real-time monitoring and continuous management of logistics processes. In this study, we propose a method of estimating the service completion time of key processes based on process-state information collected in real time. We first identify the factors that influence the process completion time by modeling and analyzing an influence diagram, and then suggest algorithms for quantifying the factors. We suppose the container terminal logistics and the process of discharging and loading containers to a vessel. The remaining service time of a vessel is estimated using a decision tree which is the result of machine-learning using historical data. We validated the estimation model using container terminal simulation. The proposed model is expected to improve competitiveness of logistics systems by forecasting service completion in real time, as well as to prevent the waste of resources.