In recent years, content integrated language education has taken center stage in Japanese university English-as-a-foreign-language (EFL) settings. The emphasis on content has created an opportunity for students to demonstrate analytical thinking, assessment, inference, and problem-solving skills through oral communication activities in English (L2). However, the opportunity may be perceived as a challenge by students, who were exposed to teacher-centered pedagogy during their pre-tertiary language education and raised with cultural values that conflict with the expectations. Therefore, some students may remain disengaged or give short answers when they are asked to demonstrate critical thinking. Students' lack of response is often misconstrued as the absence of critical thinking, leading to a misconception among language educators. The present article attempts to offer insights into the challenges facing Japanese EFL students when they attempt to demonstrate critical thinking and emphasizes the role of language teachers' intercultural competence in understanding the challenges students experience and proposes learner autonomy as a critical step towards overcoming this challenge.