 As a colonel, he commanded the 11th Artillery Regiment between 1887 and 1891.Promoted to Brigade General in December 1891, he commanded the 48th Infantry Brigade between 1891 and 1897, then the 19th Artillery Brigade.In 1898, Chanoine, his former senior officer in the Japan mission, was Minister of War and Brunet became his Chief of Staff (""Chef de l'état-major du ministre de la Guerre"") with the rank of Divisional General.