He served as midshipman on the cruiser Matsushima on its long distance navigational training cruise to Honolulu, Hilo, Wellington, Brisbane, Palm Island, Queensland, Batavia, Singapore, Mako, Tsingtao, Port Arthur, Dairen, Chemulpo, Chinkai, Busan and Kagoshima. On his return, he was commissioned as ensign and assigned to the Katori, followed by Otowa and Suma.
After further attendance at the Naval War College (Japan), Koga held shore staff posting following his graduation and promotion to lieutenant commander in 1917. In 1920, seeing no action during World War I, Koga became a resident officer in France. He returned in 1922 to become executive officer on the Kitakami. On his promotion to captain on 1 December 1926, Koga was again posted to France, where he served as a naval attaché in Paris until 1 November 1928.
Recalled to Japan in 1930 and being given command of the Yokosuka Naval Station, Koga captained the heavy cruiser Aoba from 31 December 1930, and the battleship Ise from 31 December 1931, until his appointment to rear admiral on 31 December 1932 and transfer to be Chief of the Imperial Japanese Navy General Staff's Intelligence Division in 1933.
Commander of the IJN 2nd Fleet in 1939, Koga was placed in command of the China Area Fleet on 1 September 1941. Koga shared Yamamoto's misgivings about war with the United States, but disagreed with Yamatoto regarding the use of naval aviation, remaining a firm battleship advocate until events later in the Pacific War proved his position outdated.
With the start of the Pacific War, Koga commanded naval operations during the capture of Hong Kong from 9 December-31 1941. Following the death of Admiral Yamamoto Isoroku on 19 April 1943, Koga succeeded Yamamoto as Commander in Chief of the Combined Fleet. His flagship was the battleship Musashi.
Koga attempted to revitalize Japanese naval operations by reorganization of the Combined Fleet into task forces built around aircraft carriers in imitation of the United States Navy, and organized a land-based naval air fleet to work in coordination with the carriers. Operationally, he intended to mount an aggressive counteroffensive in the Aleutians to dilute American forces and to lure the American fleet into a major naval engagement in 1943. However, the losses of Japan's land and carrier based aircraft based in the central Pacific eventually forced a Japanese withdrawal from the Gilbert Islands and Philippines by the end of the year. Koga gradually adopted a more conservative stance, attempting to conserve his remaining forces to inflict maximum damage on the Americans when they closed toward the Philippines.
Koga was killed when his plane, a Kawanishi "Emily" flying boat, crashed during a typhoon between Palau and Davao while overseeing the withdrawal of the Combined Fleet from its Palau headquarters on 31 March 1944. His death was not announced until May 1944 when he was formally replaced by Admiral Soemu Toyoda.