From April 1900, Samejima was commander of Yura Fortress and from May 1902 was commander of Tokyo Bay Fortress, becoming a lieutenant general in September 1904. In December 1904, he was appointed commander of the newly created IJA 11th Infantry Division and was sent to the front lines as reinforcement to General Nogi Maresuke’s Japanese Third Army at the Siege of Port Arthur in the Russo-Japanese War. The 11th Division subsequently became the core of the new Japanese Fifth Army at the Battle of Mukden. In April 1906, he was awarded the Grand Cordon of the Order of the Rising Sun and in June 1906 was transferred to command the IJA 14th Division.