【For Japanese Government Funded Foreign Students: MEXT Scholarship Students
(The Ministry of Education, Culture, Sports, Science and Technology Scholarship Students 】

Japanese Government Scholarship Students are able to enter Japanese universities receiving exemption of the entrance examination fee, matriculation fee and tuition fee, and are granted a scholarship stipend every month. Graduate School of Science/School of Science accepts 42 MEXT scholarship students from 22 countries as of May 2013.
This section provides brief information on MEXT scholarship procedures and schedule.

See also following links.

After finishing high school in a foreign country, a person wishing to enroll in a undergraduate course as a Japanese Government Scholarship Student should apply for the Japanese Government Scholarships for (Undergraduate) Students recruited by Japanese Embassies and Consulate Generals abroad.
If accepted, the applicant must take Japanese language lessons at Tokyo University of Foreign Studies or at the Center for Japanese Language and Culture at Osaka University for a year.
If the applicant passes the screening of the university for which she/he is applying, the applicant can enroll in the undergraduate course of the university.

An applicant usually enrolls under the status of research student and works in research activities for six months to a year. After passing the entrance examination,
the applicant enrolls in a master’s or doctor’s program.
Applicants who have an insufficient level of Japanese must take a 6-month Japanese training course at the International Student Center （required to enroll in as a MEXT research student）.