Previous studies with native English speakers have shown that working memory capacity and the inhibition function of the central executive plays an important role in understanding and producing metaphors. Results also show that phonological short-term memory capacity affects metaphor comprehension. However, to date no studies have investigated the cognitive processes behind the comprehension process of metaphors in native Japanese speakers. Therefore, this study focused on reinvestigating the results of previous studies by examining the effect of working memory capacity and phonological short-term memory capacity on the comprehension of metaphors by native Japanese speakers. Working memory capacity and phonological short-term memory capacity were independent variables and the comprehension rate and reaction time were dependent variables. Thus, it was found that working memory capacity does not affect the comprehension rate in native Japanese speakers but affects the time required for comprehension. Participants with larger working memory capacity could comprehend metaphors faster that those with a smaller working memory capacity. Phonological short-term memory capacity was found to effect neither the comprehension rate nor reaction time. Furthermore, it was found that the type of metaphor affects the comprehension time and metaphors are understood faster than similes. Thus, metaphors are comprehended as categorical sentences while similes are comprehended as comparison sentences.