Thank you very much Lawrence for your explaination about Monbukagakusho . Are you applying mext this year or you had applied it ?Hey Ichiko. Glad to see you interested in studying in Japan! There a few things you need to think about first. The most important thing to think about is what you want to study. If you want to be an undergraduate then simply look at the major you want to study, look at the location, and find the school with the highest reputation or school that is most meaningful for you. At that point it is simply a matter of applying for the school.
If you want to be graduate student then there is a bit more work. It is important to look at the school and location but even more important is research or lab you will work in. I recommend doing the same steps as undergraduate and then when you decided which schools you would like to apply to, look at the faculty pages to find out the research each professor of your major is doing. Find out which research topic appeals to your interest or skills the most and then read a few papers by that professor. Once you feel that you know enough about the work of the professor, then write a nice email to him inquiring about joining his/her lab. It is tough since some professors won't reply but even if they don't reply please don't pester them since more often than not, they are simply busy. Some schools require you to contact a professor after you started your application but check before hand. Eventually when you secured a position in their lab. Your professor should give you an idea of the topic of research.
Once you have completed all of this, it is time to start your application. There are two tracks for applying for MEXT. The first is embassy recommended or university recommended. One can be easier or not depending on your quota for the embassy recommended in your country. I personally did the university recommended. The paper work on these process are nearly the same except that with embassy recommended, you need to apply earlier and take exams at the embassy. The process for embassy is a little bit more work. You do all your application through the embassy. When they accept you, you will get three choses of schools that you want to go to. At that case, you need to contact the admission department of the school and the lab you want to work in and ask to become a research student. As a research student you focus on research for a year and study for entrance exam so you can actually apply for a degree program. You basically don't directly become a degree student in the school until after you take the entrance exam a year after you apply through embassy.
If you apply for university recommended it is basically the same as applying directly for the school but you need a research plan. The benefit of university recommended is that you get direct entry into the school and can get a university scholarship that is not necessarily the MEXT scholarship. (Which means if you do masters with that scholarship, you can apply for MEXT scholarship for Ph.D without the 3 year rule of going back to your home country).
If you do undergraduate, then research may not be necessary at all. It is useful to know Japanese.