A hybrid element model has been formulated to understand the wave interaction with moored ship motion using mild slope equation (MSE) including the influence of breakwaters and wave absorbers, under resonance conditions for variable bathymetry. In a hybrid element formulation, a combined approach with the finite element method (FEM) in an interior domain (port region) including moored ship region and an analytical approximation in the unbounded region (open sea) is utilized to determine the wave response of moored ship motion. Especially, in this approach, a FEM and analytical approximation are firstly utilized to solve MSE with the consideration of permeable breakwaters for moored ship motion under the resonance conditions. The non-uniform discretization pattern enhanced the numerical accuracy of the coupled numerical approach and is verified by using convergence analysis. Further, the simulation results are compared with existing studies to validate the applicability of the present numerical model. Wave absorbers and permeable breakwaters are employed to determine the incident wave response over moored ship motion inside the realistic Paradip port, Odisha, India. In addition, the efficacy of permeable breakwaters and wave absorbers on moored ship motion is investigated. It is shown that breakwaters and wave absorbers at appropriate locations play a significant role to induce/reduce the resonance inside the port. Therefore, the current numerical model provides the countermeasures tactics such as installing breakwaters, wave absorbers to mitigate the resonance in arbitrarily shaped ports for safe moorings.