After the Battle of Ueno, Murata led the second platoon to support the Tosando force, and on July 15, he participated in the battle to recapture Shirakawa (in charge of Tanakuraguchi) and the battle of Nihonmatsu, and then the siege of Aizu Wakamatsu-jo Castle.
上野戦争の後は二番小隊を率いて東山道軍の応援に赴き、5月26日の白河奪還戦（棚倉口を担当）、二本松戦を経て、会津若松城攻囲戦に参加した。