Jenkins (2000, 2002, 2006) attempts to establish the Lingua Franca Core features of English, or phonological features crucial to achieving mutual intelligibility in a lingua franca situation, but she does not focus upon Japanese-influenced variations of English. This paper aims to identify phonological “errors” found in Japanese science major student-researchers’ speech which might lead to miscommunication. Through the analysis of the transcription of Japanese-influenced speech, it is argued that the following three types of mispronunciation would seriously impede intelligibility: (1) mispronunciation of consonants such as plosives and liquids; (2) vowel length alternation; (3) misplaced or absence of word stress. These findings may offer implications for English language teaching, especially the prioritization of phonological instructions.