In the course of a biographical sketch of Joseph Hardy Neesima (Niijima Jō), 1843-1890, Glenn Sunshine also lays out the background of Christianity in Japan, including this:
Unfortunately, the missionaries made two mistakes that would cost the Catholic Church in Japan dearly. First, the Spanish arrived and promoted the Franciscans and Dominicans as rivals to the Portuguese Jesuits in a bid to get their own trading concessions in Japan. Second, the Jesuits had all the converts take on Portuguese names and begin wearing Western clothing. Both of these had the effect of making the missionaries look like they were covertly advancing colonial interests, and the converts look like foreign agents.
As a result, there were outbreaks of persecution in 1597, 1613, 1630, and 1632. After a rebellion in 1637-38, Christianity was officially outlawed and Japan closed off to all foreigners except the Dutch. About 30,000 Catholics continued to worship in secret as kakure kirishitan (“hidden Christians”), only coming into the open after the Meiji Restoration in the mid-1800s, when Japan allowed freedom of religion.