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PurposeThis paper examines how the altering nature of planning decisions affects operational efficiency in seaport container terminals. The uncertainty and the role of the planner were investigated considering the dynamic integrated planning function of the quay to yard interface.Design/methodology/approachA System Dynamics model has been built to illustrate the integrated dynamic environment. Data collection was conducted at a leading container terminal at a hub port. The model was simulated for different scenarios to derive findings.FindingsThe planner has been identified as the agent who makes alterations between the initial operational plan and the actual plan. The initial plan remains uncertain even when there is no impact from crane breakdowns, requiring a significant number of alterations to be made. The planner who had worked on the yard plan had altered (approximately 45%) the initial plan than the alterations done by the planner who had worked on the vessel plan. As a result, the feedback loop that is created by the remaining moves at each hourly operation influences the upcoming operation as much as crane breakdowns influence.Originality/value The uncertainty and the role of the planner were investigated considering the dynamic integrated planning function of the quay to yard interface. The findings of this study are significant since terminal efficiency is examined considering the quayside and landside as an integrated system.