The aim of the current study was to investigate whether obese subjects have different insulin secretory capacity compared to lean subjects with the same glucose tolerance in a Japanese population. We included a total of 1749 Japanese employees who underwent 75-g oral glucose tolerance test (OGTT). The study population was divided into deciles of 120-min glucose levels and the indices of insulin secretion and insulin sensitivity in each decile were compared between the subjects with and without obesity (body mass index ≥ 25 kg/m2). The indices used in the current study were Matsuda index, insulinogenic index, and disposition index. Obese subjects had significantly lower values of Matsuda index and significantly higher value of insulinogenic index than non-obese subjects in every decile (all p < 0.05). On the other hand, disposition index was not significantly different between non-obese and obese subjects in any decile of 120-min glucose level (all p > 0.05). Similar findings were observed when the study population was classified by waist circumference. In conclusion, disposition index derived from the data of 75-g OGTT was similarly decreased in obese Japanese subjects compared to non-obese Japanese subjects with the same post-load glucose levels. Future studies will be needed to confirm whether the development of glucose intolerance in obese Japanese subjects is accompanied by the same degree of pancreatic beta cell dysfunction as non-obese Japanese subjects.