The Kyoto City Magistrate controlled Nara's administration and justice by issuing commands while the Nara Magistrate was in charge of temples and shrines having domains authorized by the bakufu.
京都町奉行の命令は、奈良の行政、司法を差配し、奈良奉行が受け持ったのは、朱印地を持つ寺社であった。