However, from around Meiji Restoration the Shibamura Domain distanced itself from the bakufu and became cooperative with the new government; after the Restoration it was asked by the new government to control the property of the government within Yamato Province together with Takatori Domain.
しかし明治維新頃から幕府より離れて新政府側に与し、維新後は高取藩と共に大和国内における御料の取締りを命じられた。