There is a theoretical debate regarding whether children represent God with reference to a human. Most previous studies have assessed this issue focusing on knowledge/omniscience in western children. This study used a theoretical framework characterising mental capacities in terms of motivational/emotional (experience) and cognitive (agency) mental capacities and tested whether Japanese children discriminated between God, a human, a baby and an invisible agent according to these capacities. Three- to 6-year-old children were asked about the experience and agency of the agents. The results revealed that children discriminated God from a human in terms of mental capacities including experience and agency in 3-year-old children. On the other hand, 4- to 6-year-old children, but not 3-year-old children, discriminated a human from a baby and an invisible person. The results suggest that the Japanese children's representations of God differed from their representation of a human during preschool years.