From 1893-1896, Batyanov was commander of the 12th Army Corps in the Kiev Military District. He introduced many innovations, including rapid-fire weapons (machine guns) and new tactics, placing strong emphasis on modernization of training. For this, he earned the strong disapproval of his superior, General Mikhail Dragomirov, who forced Batyanov into the reserves. However, Batyanov was reinstated only a year later, this time as commander of the 16th Army Corps, which he again attempted to modernize. In 1903, he was promoted to General of Infantry and appointed to the Military Council. During the Russo-Japanese War, he was appointed commander of the Third Manchuria Army in May 1905, replacing General Alexandr von Bilderling after the Battle of Mukden. He helped organize a new defensive line north of Mukden against a possible further Japanese offensive.