How the State Dealt with Minority Populations:
Social Outcasts:
During the rule of the Tokugawa Shogunate, there were a select few minority populations who lay outside of the caste system, the eta and hinin, or the filthy and the untouchable. In order to handle these outcasts, the government restricted them to work and live in specific urban districts, so that they could be contained. Along with prohibiting them from traveling outside of their given districts, however, the government actually managed to make use of these minorities. People from these minorities were given jobs that either no one else wanted, or that no one else could take part in due to religious reasons, such as working as an executioner, or preparing meat. Thus, by giving them these unwanted but still necessary jobs, the government made these outcasts into an essential part of society.
Religious Minorities:
The Tokugawa Shoguns were not keen to have western religions grow in Japan and disrupt their rule's stability, which they had worked so hard to create. Thus, after trade with the Spanish and Portuguese had brought missionaries who converted portions of the population, the shogun enforced a ban on foreign religions, namely Christianity. Those who belonged to the christian minority were imprisoned, and even executed, forcing any Christians who remained to keep their religion in secret. The shogun even went as far as to begin outlawing trade, in order to avoid bringing more missionaries into the state. Trade was eventually banned completely, and Japan turned to an isolationist policy, in an attempt to keep out Christianity and other unwanted foreign ideas for the remainder of the period.