To construct a seismic hazard map for intraplate earthquakes in Japan, historical records, paleoseismology data and a time-dependent conditional earthquake recurrence model were combined to create two types of contour maps: a probability map of peak ground acceleration (PGA) of 0.2 g or higher between 2001 AD and 2050 AD, and a PGA map of 10% probability during the same period. The resulting maps demonstrate the effectiveness of conditional seismic hazard analysis, although there are several uncertainties in the estimation of the slip rate, the elapsed time, and the segmentation of seismogenic fault systems. To create these maps, the historical seismicity rate for the last 400 years, and synthetic earthquake frequency from active fault data are first compared to examine the effect of uncertainties in fault segmentation and slip rate estimation. Then hazard maps based on time-dependent and time-independent models are derived. The results suggest that the conditional hazard map shows better agreement with current understanding of the recurrence behavior of active faults. For example, (1) low probabilities are obtained for faults that are considered to have ruptured within the historical period, and (2) higher probabilities are calculated for faults with long elapsed times or high slip rates. In addition, some seismogenic active fault systems are indicated as precautious faults based on the time-dependent earthquake recurrence model.