Since Nobunaga's entering the capital in 1568, Naomasa became mainly in charge of government affairs in the Kinai region (provinces surrounding Kyoto and Nara), and served as obugyo (shogunate administrator)(supervisory role) at the time of granting of nanjatai (granting of a fragrant wood which is said to have the best aroma).
永禄11年（1568年）の信長入京以降、主に畿内の政務を担当し、蘭奢待下賜の際の御奉行（監督役）を務めた。