The Kyoto Gundai was also put in place to govern Kyoto and the surrounding area, but later split into the Kyoto Machibugyo, which was responsible for the city, and the Kyoto Daikan, which managed the surrounding area, the Imperial Household territory, and the Court Noble territory there.
また、支配下に京都とその周辺の行政のために京都郡代が置かれたが、後に町中を担当する京都町奉行と周辺部やそこにある皇室領・公家領を管理する京都代官に分離するようになった。