I think you have your terms confused. "Nissei" refers to second-generation Japanese immigrants living outside of Japan. The term you are looking for is "Yamato", which refers to Japan's dominant ethnic group.

Yamato Japanese have been culturally distinct from other ethnic groups in modern-day Japan for a long time. One historically important non-Yamato group were the Emishi, who may be ancestors of the modern-day Ainu. There are written records of the Emishi going back to the 5th century, when a Chinese text referred to them as the "Hairy People". As the Yamato polity expanded across Honshu, the Japanese fought the Emishi and eventually subjugated them.