A numerical model to solve mild slope equation is developed by use of a preconditioned conjugate gradient method (PCGM). In the present paper. accurate boundary conditions and a better preconditioner are employed which are improved from the existing method of Panchang et al. (1991). Computational procedures are focused on weakly nonlinear waves, and emerged problems to make a more accurate model are discussed. The results of model are tested against laboratory results of both circular and elliptic shoals. Model results of wave amplitude show excellent agreement with laboratory data and thes thus model can be used as a powerful tool to calculate wave transformation in shallow waters with complex bathymetry.