A magnetically semi-implicit finite-difference time-domain (FDTD) scheme based on the scattered-field formulation in cylindrical grids is presented. This semi-implicit FDTD scheme has a longitudinally zero-dispersion property and calculates only the electromagnetic field (wake field) scattered on the walls of an axially symmetric accelerator structure. As a result, the presented scheme does not include directly an ultra-relativistic bunch current in its formulation. This scheme is applied to the wake field simulation of a beam dechirper with a realistic model of bunch charge density. A linear chirp at the uniform part of the charge distribution is reproduced in this simulation. Dependencies of the dechiper length and the geometry parameters of rectangular corrugation on the wake potential are discussed in a parameter study with the presented FDTD scheme.