From 1939 to 1940, Nakai served on the senior staff of the IJA 21st Army tasked with the Canton Operation, and from February 1940, on the senior staff of the IJA 22nd Army, a garrison force in Guangxi which fought at the Battle of South Guangxi and which was disbanded for its insubordination in invading French Indochina.

After a brief stint as an instructor at the Toyama Army Infantry School, Nakai was assigned the post of chief-of-staff of the IJA 20th Division, based in Korea.

In January 1943, the IJA 20th Division was transferred to the Japanese Eighteenth Army in the Southern Area Command (eastern New Guinea).

On the death of General Shigeru Katagiri in April 1944, Nakai became acting commander of the IJA 20th Division.

He and his surviving forces held out against the Australian Army in the Markham, Ramu and Finisterre campaigns and other combat operations in New Guinea until the end of the war.