Common ways
A lot of people go to Japan by various methods. I have met a lot of normal language learners that use the Jet Program. I went to a Christian college there named Tokyo Christian University. Some people go with Language school programs. I recommend praying and asking God for opportunities, but these might be a place to start.
Jet Program
The Jet program is an English teaching program. This is basically a full time job. This would allow you to get involved in a church on Sundays and opportunities with said church. I will leave a link to the program here. https://jetprogramusa.org/
Language Schools
There are plenty of Japanese language schools in Japan. This is a good option because this allows you to pick where you want to be in Japan. I will make a list of some here.
ALA School (Tokyo)- https://ala-school.jp/ They are based in Tokyo. They are in Shinjuku City which is downtown Tokyo. There are a few churches in the area. For example, Shinjuku Shalom Church, Tokyo Lutheran Church, Okubo Baptist Church, Yodobashi Church, Etc. Look up “Churches in Shinjuku” for more.
GogoNihon (Over 10 Locations)- https://gogonihon.com/en/schools/. One of them is in Okayama. That is very much the countryside. (Think rice fields!) I went to a church near there called Takashima Chapel. They are a lovely church!
This link shows more options, https://www.japan-guide.com/school/. Take a look around on Google to see if something is a better fit for you!
Christian Colleges
TCU Tokyo Christian University– https://www.tci.ac.jp/english/. I went here! They have short and long term programs! There are pros and cons. I will probably write another post about this school alone. It is in Chiba, Inzai. Beautiful city and campus. However, it is about an hour by train to downtown Tokyo.
International Christian University–https://www.icu.ac.jp/en/. They provide a lot of housing here. They also have both short and long programs. One of those is just a week long, so it seems. They are in downtown Tokyo area. Very close to Shinjuku City.
Tokyo Woman’s Christian University–https://www.twcu.ac.jp/main/english/index.html As the title says, it is a university for women. They offer summer and spring language programs for international students. It is very close to Kichioji Station in Tokyo.
Again, Please do more research. These are just the schools I have heard about.
1st-12th Schools
Waseda International Christian School- They have a website but I am unable to link it here. They are also located in the downtown Tokyo area. They offer school for 1st through 12th Grade. This would be good for missionary kids. Just thought I would add this in real quick, as it is school related.
YWAM- Youth with a Mission
I have been to a YWAM in Vancouver Canada, we were going to do our mission trip to Japan but I had to leave early. (Might also share about this in another post.) A lot of people will go to the YWAM in Japan. I knew one of the leaders because he went to my church. Little Ones’ Mission International School. Yes it is a church! It is bilingual and also referred to as LOMIS. Anyway, that leader was super nice and had a heart for Japan and razing up missionaries. I will leave a link to them here. https://www.ywamjapan.org/en/
I am sure there are plenty more ways to go but these are the most common and the easiest way to get your feet wet! Hope this opened up new ideas!