I’m not super knowledgeable on the topic, but aside from there being immigrants and people of various ethnicities living in Japan, there is also this:

Early in the Meiji period, the Japanese government consolidated its hold on the peripheral islands of the Japanese archipelago. In the territory inhabited by the Ainu, the Meiji regime tried to wipe out markers of Ainu ethnicity (earrings and tattoos, for example) and prohibited the Ainu from practicing their religion or hunting in their ancestral hunting-grounds. In 1899, the state enacted the “Law for the Protection of Former Hokkaidō Aborigines,” which removed land from communal control, thereby forcing the Ainu to become petty farmers. Japanese assimilation policies not only dispossessed the Ainu, they destroyed nearly all indicators of Ainu cultural and ethnic identity. The Japanese government also embarked on a policy of cultural assimilation in Okinawa, paying particular attention to discouraging the use of the native Okinawan language and enforcing the use of standard Japanese among schoolchildren. (PW)

https://en.wikipedia.org/wiki/Ainu_people

The Ainu went from being a relatively isolated group of people to having their land, language, religion and customs assimilated into those of the Japanese.[35] Their land was distributed to the Yamato Japanese settlers and to create and maintain farms in the model of Western industrial agriculture. It was known as “colonization” (拓殖) at the time, but later by the euphemism “opening up undeveloped land” (開拓) […] This discrimination and negative stereotypes assigned to the Ainu have manifested in the Ainu’s lower levels of education, income levels and participation in the economy as compared to their ethnically Japanese counterparts.

https://en.wikipedia.org/wiki/Ryukyuan_people

Although officially unrecognized, Ryukyuans constitute the largest ethnolinguistic minority group in Japan, with 1.4 million living in the Okinawa Prefecture alone. […] United Nations special rapporteur on discrimination and racism Doudou Diène, in his 2006 report,[25] noted a perceptible level of discrimination and xenophobia against the Ryukyuans, with the most serious discrimination they endure linked to their opposition of American military installations in the archipelago

Okinawa was an independent kingdom until being colonized by Japan in 1879. The Empire of Japan suppressed Okinawan language and culture. The United States invaded Okinawa in April 1945. […] The United States occupied Okinawa until 1972, when it became a prefecture of Japan. (PW)