Navigation safety is further emphasised for terrain referenced navigation (TRN) systems used in middle-range unmanned aerial vehicles (UAVs) than those in cruise missiles flying through mountainous areas, because middle-range UAVs may fly to regions and cities containing both combatants and civilians. For safety assurance of TRN systems, this paper proposes a method to compute protection levels (PLs) to assure the required level of integrity under nominal conditions. For obtaining PLs of TRN systems, all the components of the TRN measurement errors should be identified and overbounded. This study models every error component: the radar altimeter error, the vertical error in the terrain elevation database, the lateral offset induced error, and the interpolation error. Based on the characteristics of TRN systems using terrain information for obtaining navigation solutions, this study developed new models for the lateral offset induced error and the interpolation error as a function of terrain roughness by examining the effect of terrain roughness on the error sources. The simulation results demonstrate that the latitude and longitude PLs obtained by applying the proposed models can sufficiently overbound the navigation solution error for TRN systems under nominal conditions; especially the proposed method shows remarkable performance in regions with low terrain roughness.