In coastal engineering, one of the main problem experienced by the large port with ship operation is moored ship motion due to the exterior long wave activities. To control the wave induced vessel motion inside port, accurate estimation of spectral wave response behavior in the port due to the multidirectional incident waves is essential. For this, a numerical model has been formulated using the finite element method with governing equation as mild slope equation. The model incorporates different boundary conditions: permeable breakwater, fully or partially absorbing wall boundary conditions. The numerical model is verified and validated with existing experimental and analytical approximations. The numerical scheme has been applied on Paradip port, Odissa, India and the variations on wave spectrum due to the incident wave in the port basin with and without including breakwater has been investigated. Based on simulation analysis, measures to attenuate the water wave oscillations inside port basin under the resonance state are discussed