A visa must be acquired in order to study in Japan. There are two ways in which the visa may be acquired.
An representative of the educational institution in which the foreign student is scheduled to enroll makes an application to the relevant immigration office, etc. for a Certificate of Eligibility for Residence Status (“Certificate of Eligibility”) on the foreign student’s behalf. Once the Certificate of Eligibility is granted, the foreign student wishing to enter Japan takes his/her Certificate of Eligibility to an overseas Japanese embassy or consulate and files an application for a visa.
See the simple diagram as bellows: