From Emperor of Japan: Meiji and His World, 1852–1912, by Donald Keene (Columbia U. Press, 2005), Kindle pp. 109-110:
Now that the long-debated issue of the port of Hyōgo [Kobe] had at last been settled, on July 7 the shogunate further decided to permit foreigners to conduct business in Edo and Ōsaka. With this, full compliance with the provisions of the treaties signed with the foreign nations had been achieved. This did not signify that all the shogunate’s problems had been solved: major and minor problems constantly arose, and increasingly the young emperor was obliged to take part in decisions.
One minor problem arose as a direct consequence of the foreign settlements. On July 14 the Nagasaki magistrate arrested and imprisoned sixty-eight Christians. Christianity had been prohibited in Japan for about 250 years, but “hidden Christians” in the region of Nagasaki had preserved the religion without guidance from ordained priests or even from Christian books. Over the years the beliefs of these Christians had steadily drifted from orthodox teachings, and by now the hymns they sang, originally in Latin, had become gibberish, memorized by believers who had no idea of the meanings. Most of the Christians were poor fishermen and peasants. If suppressing such a cult had been a purely religious matter—if, say, it involved a heterodox Buddhist sect—it could have been achieved without difficulty, but the suppression of a Christian sect immediately involved the foreign powers, which were highly sensitive to attacks on their religion.
As far back as 1857, as the result of negotiations between Townsend Harris and the senior councillor Hotta Masayoshi, it had been agreed that foreigners should be able to practice their religions without hindrance, and the Americans obtained permission to erect a Protestant church in the foreign settlement. At the same time French priests were active in promulgating Catholicism, especially in the area of Nagasaki. The hidden Christians, overjoyed by the arrival of coreligionists, openly visited the church erected by the French and appealed to the French minister for support. Some, rejoicing that their hour had at last come, flaunted their new importance, leading to conflicts even within families. Buddhists, angered by the government’s slowness in punishing the Christians, even though the religion was still prohibited, threatened to take matters into their own hands and kill the Christians. The latter responded by arming themselves with bamboo spears. After the arrests on July 14 the French and Portuguese consuls in Nagasaki demanded the release of the Christians and, when this was refused, reported the matter to their legations, urging them to negotiate with the shogunate for release of the prisoners.