The ecumenical movement and the desire for church union have deep roots in Japanese Protestantism. In 1872 the first Japanese Protestant church, the Nihon Kirisuto Kokai (Church of Christ in Japan) was founded on a non-denominational basis. The ReformedPresbyterian denominations had formed a union in 1877, the Anglicans in 1887, and the Methodists in 1907. However, the creation of a single Protestant denomination in 1941 with the formation of the Nihon Kirisuto Kyodan (the United Church of Christ in Japan) remains one of the most controversial issues in the history of Japanese Protestantism. This Protestant union was seen by some as an answer to prayer with the fulfilment of a long-term ideal. To others the union was viewed as being the result of bowing to the demands of ultra-nationalism, and of the Christian leadership sacrificing personal principles in the name of national solidarity under government pressure. During the late 1960s, the issue of the war responsibility led to a major crisis within the Kyodan.
The formation of the Kyodan took place during a dark age in Japanese religious history, reminiscent of the witch hunts of European medieval history, which began after the 1931 Manchurian incident. Paralleling the steady rise of Emperor-centred militarism, there was the callous persecution of religious groups, notably new religions such as Omoto but some Christian groups were not spared including the Holiness Church, Plymouth Brethren, the Seventh Day Adventists, the Salvation Army and the Nihon Seikokai (the Japan Anglican-Episcopal Church) because they were deemed by the authorities to hold heterodox ideas or were too closely identified with foreign countries. After the opening of the SinoJapanese War in 1937, the government pressed ahead with the union of religious groups, including Protestant churches, in order to enhance its control over religious organizations. In April 1940, the Religious Bodies Law came into effect and all religious bodies had to obtain new government charters. By late 1940 it was evident that the government's intention was to combine all Protestant denominations together in a single church. This led to the creation of the Kyodan, which received government recognition in December 1941.
The new union church had a centralized leadership under a director, a single General Conference and twelve regional conferences, which included Taiwan and Korea, and Manchuria (a missionary conference) as well as metropolitan Japan. Initially, it possessed a sectional structure that allowed the joining denominations to retain a degree of autonomy. Its creedal commitments maintained the traditional emphasis and basis of Universal Christendom by making the Old and New Testaments its standard of faith and practice, and placing the historic Apostles' Creed at the centre of its Confession of Faith. In the discussions leading to the formation of the new church, its faith had taken second place to the formulation of its organizational structure.
With the end of the Second World War in 1945, a new era began in Japanese Christian history in which there was complete religious freedom. Even though a significant number of former Anglicans, Reformed-Presbyterians, Lutherans, Baptists, and others left to reestablish their former denominations, the majority of Protestants chose to remain within the Kyodan. A positive image of the Church was created by the work of its ministers and social agencies in helping ordinary Japanese recover effects of dislocation caused by the war. However, the Kyodan's growth was hampered by its dependency in the early postwar years on overseas financial support and also by the general perception that Christianity was a foreign religion not suited to the religious proclivities of ordinary Japanese. Most Japanese still perceived Christianity as not offering a viable religious alternative. The Kyodan continues to wrestle with the question of making its Christian message more relevant to the concerns of a rapidly changing Japanese society. In the past, Christian schools and universities have played a significant role in the Japanese educational system. However, lack of Christian academic staff and shortage of ordained ministers has led to an erosion of Christian influence at Kyodan associated universities and schools like Aoyama Gakuin, Doshisha, Kwansei Gakuin, Meiji Gakuin, and Tokyo Joshi Daigaku. The Kyodan faces a serious challenge in attracting young people into it for the church membership is rapidly aging. Even so, the Kyodan remains the largest Protestant denomination with over 200,000 members with a nation-wide network of churches and strong international links.