The KiK-net ground motion database is used to develop ground motion prediction equations for Arias Intensity (I_a), 5-95% Significant Duration (Ds_5-95), and 5-75% Significant Duration (Ds_5-75). Relationships are developed both for shallow crustal earthquakes and subduction zone earthquakes (hypocentral depth less than 45 km). The models developed consider site amplification using V_S30 and the depth to a layer with V_S=800 m/s (h₈₀₀). We observe that the site effect for I_α is magnitude dependent. For Ds_5-95 and Ds_5-75, we also observe strong magnitude dependency in distance attenuation. We compare the results with previous GMPEs for Japanese earthquakes and observe that the relationships are similar. The results of this study also allow a comparison between earthquakes in shallow-crustal regions, and subduction regions. This comparison shows that Arias Intensity has similar magnitude and distance scaling between both regions and generally Arias Intensity of shallow crustal motions are higher than subduction motions. On the other hand, the duration of shallow crustal motions are longer than subduction earthquakes except for records with large distance and small magnitude causative earthquakes. Because small shallow crustal events saturate with distance, ground motions with large distances and small magnitudes have shorter duration for shallow crustal events than subduction earthquakes.