This paper describes a numerical analysis of pore water pressure responses in seabed. The numerical method is developed by introducing a constitutive equation for soils and Biot's consolidation theory into the finite element method. The constitutive equation is based on Fukutake model. Fukutake model can consider dilatancy behaviour of soils under cyclic loads by employing R-O model and Bowl model, and it can simulate soil behaviours under seismic loads. However, it cannot consider the effect of axial stress variations on the non-liner stress-strain relation of soils and the model does not satisfy the principle of frame indifference. This model is not suitable for the seabed analysis under ocean wave action, because the direction of the principal stresses varies in the seabed. Then the Fukutake model is modified and the new model can consider the stress condition of seabed under ocean wave action. The finite element model is examined by comparing with observation data in the foundation soils under a breakwater.