He was Japanese, but played for North Korea during the WC.
It's quite typical for those Zainichi from the North Korean side to stay very insular whilst they live in Japan, go to their own schools, and they would be more likely to represent North Korea in sports. Whereas South Korean Zainichi are more mixed, and you see players such as Tadanari Lee playing for Japan. Anyway, Jong Tae-Se is Gaijin, he never had a Japanese passport or citizenship.