This study investigates the effects of Japanese learners’ Korean segmental production on pronunciation evaluation by Korean native raters. Read speech from 24 learners whose native language is Japanese are transcribed at the phonemic level, and confusion matrices are generated based on the phonemic transcriptions. The deviance from the canonical pronunciation found in the learners’ speech is analyzed in terms of phoneme substitutions, vowel insertions, and consonant deletions. Each learner’s pronunciation is rated impressionistically by 5 Korean native raters. The result shows that the deviance from the canonical pronunciation is strongly correlated with the pronunciation evaluation scores. Especially, the rates of phoneme substitutions and vowel insertions which are very strongly correlated with the pronunciation evaluation scores.