Assigned to Imperial Japanese Navy General Staff as an Operations Section chief in October 1940, Tomioka continued to serve in that capacity during the first two years of the Pacific War, during which time he unsuccessfully opposed the attack on Pearl Harbor[citation needed].

He also strongly opposed Admiral Isoroku Yamamoto's plans for the Midway operation, proposing that Japan occupy the much more strategically important Fiji and Samoa island groups instead.

Tomioka also pushed for a focus on the occupation of Port Moresby in New Guinea, either as a staging ground for an invasion of Australia, or to draw out the American carrier fleet as far as possible from its home bases.

From September 1943, Tomioka served as chief of staff to the Southeast Area Fleet and was promoted to rear admiral on 1 November 1943.

Tomioka returned to Naval General Staff as the department's Operations Bureau chief in December 1944, and held that position for the remainder of the war.