To better understand the role of motivation in determining exercise participation at the population level, we performed a questionnaire survey of 385 Japanese adults (mean age: 55.0 years, SD: 10.9 years). At baseline, the motivation subscales (intrinsic motivation, identified regulation, and external regulation), self-efficacy, and enjoyment all showed significant differences across the stages of change for exercise. Intrinsic motivation and enjoyment had similar findings, with the highest scores being noted in the maintenance stage. Among the 385 subjects, 183 completed the follow-up questionnaire 3 months later. After 3 months, most of the participants (86.9%) who were in the maintenance stage at baseline remained in the same stage. The number of participants who dropped to a lower stage after 3 months was 23. The changes of exercise stage over the 3-month period differed significantly for identified regulation, introjected regulation, and motivation. There were significant time and group interactions for intrinsic motivation and identified regulation. These findings suggest the importance of intrinsic motivation and identified regulation for performance of regular exercise, as well as the role of introjected regulation for promoting behavioral change among Japanese adults.