Ministry of Education, Culture, Sports, Science and Technology gathers the number of each religious group members. The registered religious groups report the number of their believers to the ministry by self-reporting. The reported numbers are often exaggerated. The total number of the believers of all sects exceeds the population in Japan.
The following shows the number of members of major religious sects in Japan, 2015.
Table 1: Shinto believers
|Association of Shinto Shrines
Table 2: Buddhism believers
|Jodo Shinshu Hongwanji-ha
|Koyasan Shingon Buddhism
|the Shinshū Ōtani-ha branch of Jōdo Shinshū
|The Buzan Sect of Shingon Buddhism
Besides the list above, there are two big religious groups in Japan; Soka Gakkai and Happy Science. The ministry did not report the number of their believers, because they are classified as the sect which the ministry does not have to release the data.
Soka Gakkai says they have 8.27 million households believers in their web site.
I could not find a reliable data of Happy Science. The number varies depending upon the source, from 0.1 million to 10 million.
Source is Shukyo Nenkan published by Agency for Cultural Affairs.