In probabilistic seismic hazard assessment of Nankai Trough earthquakes, a ground motion prediction equation (GMPE) is used based on the shortest distance to the fault plane, assuming a uniform slip distribution over an earthquake source region (ESR). In order to incorporate the effect of heterogeneous slip distribution, the equivalent hypocentral distance (EHD) to the characterized earthquake fault model (CEFM) for tsunami hazard assessment can be used. In this study, we evaluated the characteristics and the uncertainty of intensity measure, PGV, predicted using the EHD based GMPE proposed by Si and Midorikawa (1999). First, it was found that a geometric mean of PGVs evaluated for a set of CEFMs in an ESR was almost equivalent to the PGV evaluated assuming a uniform slip distribution. Next, the prediction variance of the GMPE was decomposed into two terms related to (i) the effect of heterogeneous slip distributions and (ii) the other factors. It was found that the former term was significantly smaller than the latter. As a result, it can be said that the original value of common logarithm standard deviation, 0.23, can be used even though a heterogeneous slip distribution is considered for calculation of EHD.