At the outset of the Second Sino-Japanese War, he was assigned to the Kwantung Army, and was on the planning team for the successful Operation Chahar in northern China.

In 1940, during the preparations for the invasion of Southeast Asia, Hayashi was put in command of the Taiwan Army Research Section, tasked with investigating issues with tropical warfare.

From 1941-1942, Hayashi was Vice Chief of Staff of the IJA 14th Area Army.

After the surrender of Japan, he was held for investigation of possible war crimes and incarcerated at the New Bilibid Prison in the Philippines.

On July 4, 1953, he, along with 113 other Japanese war criminals were pardoned by President Elpidio Quirino.