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The early mission to establish the Japanese Orthodox Church depended on the Russian Orthodox Church, especially in financial matters. The war between Russia and Japan created a politically difficult situation for the church. After the Bolshevik Revolution, the Japanese government had new suspicions about the Japanese Orthodox Church, in particular, that it was used as a cover for communist Russian espionage. The second bishop of Japan, [[Metropolitan]] [[Sergius (Tikhomirov) of Japan|Sergius (Tikhomirov)]], suffered severely from such governmental suspicion, and he was forced to resign his episcopacy and died under strange circumstances on [[August 10]], 1945, five days before the end of the war. The Russian Church similarly suffered from Stalinist policy and had no ability to help the young church in Japan.
During the Fifteen Years War (1930-1945), which from 1939 to 1945 was part of World War II, Christianity in Japan suffered under severe conditions, the Orthodox Church especially. As early as the last years of Abp. Nicholas' life, the church administration considered consecration of a Japanese to the episcopacy. While over the following decades various candidates were considered, none were formally nominated for various reasons. The situation for the church changed in 1939 when the Diet of Japan enacted legislation requiring government registration of churches. The registration process meant foreigners could not serve in positions of authority within the church, although the legislation itself did not prohibit non-Japanese from such positions. Throughout 1940, the church leadership divided over how to satisfy the law, and Metr. Sergius was "retired". As the factions endorsed various candidates, one group had approached representatives of [[Russian Orthodox Church Outside of Russia]] (ROCOR), and quickly elected the [[Archpriest]] [[Nicholas (Ono) of Japan|John Ono]] for consecration as a bishop. Fr. John and his wife Vera traveled to Manchuria where both took [[monasticism|monastic]] vows and Fr. John was consecrated bishop with the name Nicholas on [[April 6]], 1941. The disagreement between the two major factions continued throughout the war. <ref>Masatoshi John Shoji, ''The Orthodox Church of Japan, 1912-1954: A Time of Troubles'', Master's Thesis, St Vladimir's Orthodox Theological Seminary, Crestwood, New York, May 2007</ref>
After the Japanese surrender, the Allied occupation had a generous attitude to Christianity, given its predominantly American composition. Control over the Church of Japan by the Soviet dominated Church of Russia was forestalled by the Supreme Commander of the Allied Powers through the efforts of Colonel Boris Pash, who was the son of Metr. [[Theophilus (Pashkovsky) of San Francisco|Theodosius (Pashkovsky)]] of the American Metropolia.<ref>Pash, Boris T., "Checkmate!," The American Legion Magazine, April, 1958, pp14-15, 42-43.</ref> As the majority of the Slavic- and Greek-Americans would attend local Orthodox parishes, Orthodoxy in Japan took a step forward. During the war, the Japanese Orthodox Church had almost no foreign contact. After the war, instead of the Russian Church, the American Metropolia, the precursors of the [[Orthodox Church in America]] (OCA) helped re-establish the Japanese Orthodox Church, and since 1946 Archbishops appointed by the American Metropolia ruled the Church of Japan. In that time, several youth who studied at the OCA's [[St. Vladimir's Orthodox Theological Seminary (Crestwood, New York)|St. Vladimir's Orthodox Theological Seminary]] in New York are now the leaders of Japanese Orthodox Church. While a minority, under the leadership of Bp. [[Nicholas (Saiama)|Nicholas]] aligned itself with the Moscow Patriarchate, and known "Russian Podvorye Orthodox Church in Japan".