In 1692 the region was placed under the direct rule of the Tokugawa Shogunate. The Jinya served as the official residence and headquarters of the Shogon’s governor, as well as a warehouse for storing taxes (which were paid in sacks of rice.) The building was actually used for government offices right though the 1960s, but has now been converted into a museum.
At one time there were 55 such Jinyas located around Japan. This is the only one that survives.