Nagata was an influential military figure in the Meiji government and the de facto leader of the Tōseiha faction during the Gunbatsu political rivalry within the Imperial Japanese Army.

Upon Nagata's return to Japan in February 1923, he was assigned to the Imperial Japanese Army General Staff, where he served as administrator of various departments, and was regarded as an expert on Germany.

According to the testimony of Lieutenant-General Kajitsuka Ryuji, Chief of the Medical Department of the Kwantung Army, at the Khabarovsk War Crime Trials in late 1949, in the 1930s, Nagata was the "most active supporter" of the program of conducting bacteriological or germ (biological) warfare put forth by Shiro Ishii.

[2] In July 1935, Nagata's political manoeuvres led to the forced retirement of Jinzaburō Masaki, the Inspector-General of Military Training and a leading member of Kōdōha.

He entered Nagata's office in Tokyo and cut him down with his sword, making no attempt to resist arrest by military police and reportedly said that he "was in an absolute sphere, so there was neither affirmation nor negation, neither good nor evil".