Japan’s manufacturing sector increasingly relies on migrant workers, yet available wage statistics do not directly compare Indonesian migrant women with Japanese women performing equivalent work. This article examines the institutional mechanisms that may shape the wage outcomes of Indonesian migrant women in Japan’s manufacturing sector without estimating a nationality-specific wage penalty or treating aggregate differences as proof of discrimination. The study employed qualitative explanatory document analysis. Its corpus comprised 30 sources, including 25 scholarly articles and five institutional publications addressing Japanese wage structures, gender inequality, migrant-employment pathways, skill recognition, and Indonesian manufacturing. The evidence primarily covered 2016–2023, while earlier publications were retained for foundational theories and later publications were used only when they analyzed the study period or reported relevant official data. Two coding cycles identified five mechanisms: migration-status and occupational segmentation; constrained accumulation of recognized tenure and career rewards; unequal conversion of human capital into recognized value; information and bargaining asymmetries; and the intersection of gender, migrant status, and national origin. Official wage benchmarks reveal substantial variation across employment and residence categories but cannot establish a direct wage differential between Indonesian and Japanese women because the categories represent non-equivalent populations. The documentary evidence is strongest regarding residence-based segmentation, tenure, and establishment-level wage structures, while evidence concerning Indonesian women specifically remains limited and indirect. The article therefore offers a mechanism-based explanatory framework rather than a causal estimate of wage discrimination. Its governance implications include improved wage-data disaggregation, portable recognition of qualifications, practical job mobility, transparent wage classification, and accessible employment information.