Kakure Kirishitan
In 1865 a group of people at Ngasaki publicly identified themselves as Christians. Soon various communities of Kakure Kirishitan or hidden Christians, were discovered in the region. Located in more remote areas where the government surveillance was at it's weakest, these communities had preserved their religion in secret for more than two centuries. Of approximately 60,000 Kakure Kirishitan discovered at that time only half chose to return to the reintroduced church. The anti Christian laws were still in effect, and many of the discovered Christians were jailed or exiled to other parts of the country. It was only in 1873 that the Meiji government withdrew religious sanctions, although freedom of religion was not specifically granted. Even the 1889 constitution of Japan guaranteed only qualified religious freedom"within limits not prejudicial to peace and not antagonistic to duties as citizens."
Catholic
Catholic activity was entrusted to the Paris foreign Mission Society until the beginning of the 20th century. A steady if unspectacular expansion took place, and by 1937, the Catholic population was reported at 118,000 with a preponderance of the faithful living in the Nagasaki region. A network of schools mostly run by religious orders, was established throughout the country. In 1913 Sophia University ( Jochi Diagaku) was founded in Tokyo; the Sacred Heart College, founded in 1915, was reorganized as a women's university in 1948; in the following year Nanzan University was founded in Nagoya.
Orthodox
In 1872 Ioann Kasatkin better known as Faher Nikolai, established a branch of the Russian Orthodox church in Tokyo. He consecrated an Orthodox cathedral in Kanda, Tokyo, in 1891 and the church still remains a landmark in the capital. Nikolai died in 1912 at which time there we about 30,000 Orthodox believer in Japan. By 1931, membership had grown to 40,000 but in recent years the numbers have declined.