Inclusive education has become a central education policies in Japan. The purpose of this study was to clarify the current situation and priority issues of inclusive education system in early childhood education in Yaeyama Islands. For these purposes, the survey using the Inclusive Education Assessment Tool（IEAT）was conducted to evaluate the special needs education system in early childhood education of Yaeyama Islands and its results were analyzed through t-test. The result have shown that have been made to focus efforts on “Improvement of human and physical environment”. And “Improvement curriculum” was raised as priority issues. As the Issues of inclusive education system in early childhood education of Yaeyama Islands, the expertise of special needs education should be guaranteed, equal opportunity should be guaranteed. These results were suggested for efforts for early childhood education of inclusive education system construction.