Promoted to rear admiral from September 1890, Tsuboi was Commander of the Sasebo Naval District to December 1892, Commandant of the Imperial Japanese Naval Academy from 1892–1893, and Commandant of the Naval Staff College from 1893-1894.
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As a Chōshū Domain samurai he took part in the defense of the city during the bombardment of Shimonoseki by European warships from September 5–8, 1864.
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That same year he received training on board the flagship USS Colorado of the American Asiatic Squadron and was sponsored by Admiral John Rodgers to attend Columbia University from April 1872 until July 1874.