The study is devoted to identifying the key issues impeding the integration of international faculty at Japanese universities via a qualitative approach. Semi-structured interviews with 40 international faculty hired in Japanese universities with various backgrounds were conducted. The interview data were analyzed based on a three-stage coding procedure, namely open, axial, and selective coding, which identifies the main themes through increasing the level of data abstraction. The study identified the key issues from work, cultural, and interpersonal dimensions in the context internal to Japanese universities, and environmental dimension in the context external to Japanese universities. Meanwhile, the study also acknowledged the perceptual differentiation of these issues depending on international faculty's backgrounds. Based on the principles of Embedded Intergroups Relations Theory, it appears that the key issues differ according to international faculty's identity (country of origins), cultural backgrounds (previous experiences in Japan), and their organizational characteristics (academic ranks and disciplines). In other words, junior faculty in the Humanities who were not from countries in which Chinese characters are historically used or without previous experiences in Japan tend to perceive themselves as tokens at Japanese universities. Theoretical and practical implications including policies, future studies, and support systems are offered for policymakers, researchers, and university administrators.