Having stayed in Japan for almost 3 months now, I've met a couple of people in my language school who are aspiring to become mangakas in Japan. This may sound like wishful thinking, but no. They're serious. They're planning to go to college to actually study how to make manga. If you're SERIOUS about being a mangaka in Japan, this may be the most practical path towards reaching your dream.
In Japan, there are schools called senmon gakkou. They are specialized colleges that offer 2-year courses for different areas of expertise. One of which is a course in manga creation. Most of my aspiring mangaka friends are going to attend a senmon gakkou after they're done with language school.
The tuition fee is about 1 million yen a year (that's around $10,000). It'll depend on which school you go to. Some are a bit cheaper ($9,000ish/year); some more expensive ($12,000ish/year).
There are also a couple of Japanese universities that offer 4-year manga creation courses. Of course, the tuition fee is more expensive. I haven't really browsed through a lot of sites, but the most expensive I've seen is around $18,000 per year. I saw another one that was about $13,000 for the first year and $10,000 for the succeeding years.
Here's a list of the universities and colleges that offer them:
You have to be proficient in Japanese in order to be accepted into almost all Japanese universities. For senmon gakkous, it's a requirement. Foreigners who want to enter either of these two study Japanese for around 2 years at a language school (there are also shorter courses). And well, if you want to make it as a mangaka IN JAPAN, it's a no brainer that you HAVE to be proficient in Japanese.
There are many language schools here in Japan. The normal tuition fee is around $500 per month; however, it'll be a bit more expensive during your first term because of enrollment fees.
All in all, if you're serious about making it as a mangaka in Japan, these are things you have to consider. Of course it's not the ONLY way, but it seems like a more promising path: you'll be able to get a visa for up to 4 years, you'll be immersed in Japanese language and culture, you'll be taught how to make manga by a professional, and you'll be able to get important connections which may prove to be useful in the future. Are you ready to become a mangaka in Japan?