Through the 1920 and 1930s, Ōmori subsequently commanded the destroyers Namikaze, Kamikaze and Yugiri, seaplane tender Kamikawa Maru, and finally the battleship Ise from 1939–1940, while steadily increasing in rank and returning at regular intervals to torpedo school to remain expert on the latest developments in torpedo technology and tactics.

At the start of World War II, Ōmori was in command of Destroyer Squadron 1 (DesRon1), which accompanied the main strike force during the attack on Pearl Harbor.

Ōmori and his heavy cruisers narrowly escaped damage in an air raid at Rabaul, New Britain the following day, and retreated to the main Japanese base at Truk, Caroline Islands.

Ōmori was relieved of his command for having withdrawn at Empress Augusta Bay against an inferior force and was sent back to Japan.

He was director of the Special Attack Division from 13 September 1944–10 August 1945, supervising work with the Kaiten human-guided torpedoes.