As in other countries with large immigrant populations, in Japan there is increasing interest in students from culturally and linguistically diverse backgrounds who experience learning and behavioral difficulties in the classroom. The causes of the problems have not been identified owing to a lack of appropriate and comparable assessments. In this study we focused on Japanese-Brazilian elementary school students, the largest ethnic minority group of students in Japan, and explored whether evaluation of their learning and behavior is influenced by the following aspects: language proficiency, cognitive capacity and family environment. We conducted a set of tasks to assess the students' vocabulary and syntactic development in Japanese and Portuguese, and to evaluate their executive functions as an indicator of nonverbal cognitive development. Questionnaires were administered to teachers and parents in order to gain information about the children's classroom performance and family environment, such as parents' educational background and place of birth. Three key findings from our data include the following. (1) Some students in mainstream classrooms were 'at-risk' in their level of cognitive capacity. (2) Even among those with typical cognitive capacity, academic performance and classroom behavior were still rated lower than at grade level for the native population. (3) Teachers' ratings of the two aspects were associated with different factors: low academic performance was significantly influenced by poor working memory, while problematic behavior was affected by Japanese grammatical skill and father's educational background. This study used quantitative data to confirm that clear information about students' linguistic, cognitive and environmental profiles, could be used to ensure that appropriate support is provided to students experiencing difficulties.