The Vatican had set forth to win the goodwill of the Japanese Government. Roman Catholics were ordered regularly to attend some of the pagan temples and to participate in emperor-worship. In return for these and other favors, the Japanese Government made Roman Catholicism a State religion along with Shintoism and Buddhism. Many of the missioners resented the action of the Church.

In 1937, the Vatican also supported the faithful worshipping at Shinto shrines, describing this as an expression of patriotism, not religion.

In 1931 several students of St. Sophia University refused to pay homage at the Yasukuni Shrine, Tokyo. Combined pressure from the militarists and Shinto leaders once again exalted the issue of obeisance at the State Shinto shrines as the nonreligious, patriotic duty of all Japanese. Also, militarists engaged in overt anti-Catholic cam-paigns in some islands of Ryukyu and in Kagoshima prefecture.". In 1936 the Congregatio de Propaganda Fide instructed the papal delegate in Tokyo to the effect that an obeisance at the State Shinto shrine was not to be considered a religious act, and as such could be participated in by Japanese Catholics.". In the same year the National Christian Council of the Protestant Churches also publicly accepted the government's interpretation of State Shinto as nonreligious. In 1937 a group of prominent Christians offered a "Christian norito" at the Grand Shrine of Ise, asking the Shinto kami to "bring it to pass that the subjects of the empire may quicken and elevate the Japanese spirit as in the Age of the Gods;
...that they may make the sacred power of the Emperor to shine ever higher...

The issue of state Shinto involved all Christians, but its most obvious
effect was on Christian education. This impact was illustrated in 1932 in an
incident at JØchi (Sophia) University, a Roman Catholic school in Tokyo,
when a student demurred to visit the Yasukuni shrine with the rest of the
school on the ground that doing so was contrary to his religious convictions.
The extensive network of Roman Catholic schools in Japan was put in jeopardy
if the Roman Catholics did not obey government guidelines requiring
them to send their students as a body to pay their respects at shrines. The
Roman Catholic archbishop of Tokyo asked the Ministry of Education to clarify
its position on whether or not going to a shrine was considered a religious
obligation. The Ministry’s reply was that the student visits to a shrine were
based on educational considerations and that the statements the children were
required to make on these occasions were simply meant to indicate their
patriotism and loyalty (Gonoi 1990, 294–6). Furthermore, the ministry reinforced
its argument by pointing out that it would contravene its own 1899
instruction on keeping religion outside the scope of general education if students
were asked to take part in a religious exercise.
The position taken by the Ministry of Education satisfied the Roman
Catholic authorities. Indeed, it was thought that the Roman Catholic
Archdiocese could congratulate itself for having reached with comparative
ease a satisfactory solution to an important question of principle.
[Mark R. Mullins. Handbook of Christianity in Japan, 2003. P. 85]