The administrative control established in Yamato is called the uji-kabane system. Uji is usually translated as "clan" in English. The uji are seen as extensions of original agricultural communities. Essentially, farming communities were associated into groups, united by the belief that harvests would be bountiful if proper respect was paid to the group's ancestral deity (kami). Heads of the community functioned as priests, mediating the relationship between the group and its deity. As clans joined together--for instance by conquest--vertical relationships began to develop between heads of the communities and the queen or king at emergent courts. By the 5th century, these groups, possibly already called uji, were drawn together into economic, military, religious and familial ties with the Yamato kings. Some scholars have even argued that uji were purely political units, so designated by the Yamato ruler. Uji appeared first in the Nara Basin, in close association with the court; as the Yamato kingdom developed greater power, uji appeared in other areas as well.

By the 5th century, the Yamato ruler designated the chiefs of the most powerful uji, who developed close ties with the ruler over time. The Yamato court was therefore headed by a hereditary ruler, while its members came from the group of powerful clan leaders awarded kabane (titles). The two major titles were muraji and omi. Lower-ranking titles were awarded to leaders of smaller, distant clans. The highest officers of the emerging state were the o-muraji and the o-omi, the heads and representatives of those two groups.