In this paper, a modified leap-frog finite difference (FD) scheme is developed to solve Non linear Shallow Water Equations (NSWE). By adjusting the FD mesh system and modifying the leap-frog algorithm, numerical dispersion is manipulated to mimic physical frequency dispersion for water wave propagation. The resulting numerical scheme is suitable for weakly nonlinear and weakly dispersive waves propagating over a slowly varying water depth. Numerical studies demonstrate that the results of the new numerical scheme agree well with those obtained by directly solving Boussinesq-type models for both long distance propagation, shoaling and re-fraction over a slowly varying bathymetry. Most importantly, the new algorithm is much more computationally efficient than existing Boussinesq-type models, making it an excellent alternative tool for simulating tsunami waves when the frequency dispersion needs to be considered. (C) 2010 Elsevier B.V. All rights reserved.