This study aims to investigate native speakers’ perception of prosodic variation of Japanese utterances. The pitch contour above the word level is hard to determine due to individual variation or pragmatic and para-linguistic factors. Nevertheless, native speakers’ intonation is relatively consistent as long as the context and intention of the utterance is predetermined. On the other hand, L2 speakers’ intonation contains some prosodic deviation from the native speakers’ model, and yet some deviations are treated as non-native production and some are not. By identifying the prosodic deviations that are tolerated by native listeners, we will have better understanding of crucial points necessary for the improvement of Japanese pronunciation and the reference for computer-based assessment tools. The study suggests that pitch errors affect the performance score, but not as significantly as do timing errors.