Because of its valuable timber resources, the Hida Region around Takayama was put under direct control of the Tokugawa Shogunate in 1692. The Takayama Jinya served as the local government office headed by the officials dispatched from Edo (present day Tokyo).

The main building complex, built in 1816, was in official use until 1969, and is now open to the public as a museum. It includes various nicely maintained tatami mat rooms that once served as offices, conference rooms, guest rooms and residential space. There is also an interesting interrogation room.

Beside the main building stands a large storehouse built in the 1600s. This is the oldest surviving structure. Known as the biggest traditional rice storehouse in Japan, it now functions as a museum, showcasing belongings and official documents of past feudal lords, old maps of the Hida Region and historic town plans.