Although the Ainu and Japanese interacted for several centuries, the most disruptive time of Ainu-Japanese relations started after the Meiji restoration.

Prior to the Meiji restoration, Hokkaido was loosely governed from the Japanese settlement of Hakodate. There were conflicts between the Japanese rulers and the Ainu, but on a small scale.

Japanese settlers came from Honshu in a slow trickle, and established most of the major cities of Hokkaido during this time.

After the Meiji Restoration, the Imperial government took aggressive measures to settle Hokkaido and assimilate the Ainu. Ainu communities were forcibly settled, and barred from hunting. Behaviour that was "un-Japanese" was demonized by the government, while Ainu children were taken to be schooled in Japanese. Most importantly, the Imperial government expected the Ainu to become productive farmers without any sort of training or resource allocation. Most Ainu were not hunter-gatherers anymore, on the eve of Meiji Restoration, but they were definitely not farmers and, and many Ainu communities were destroyed during the settlement process.

The treatment of the Ainu by the modern Japanese state was quite similar to the treatment of many other aboriginal groups in Canada, the USA, or Australia.

Howell, David L. “Making ‘Useful Citizens’ of Ainu Subjects in Early Twentieth-Century Japan.”