The exact checklist depends on whether you’re applying for undergraduate, master’s, PhD, or non-degree/research-student status, and also whether you’re applying for a scholarship (like MEXT) at the same time. Commonly requested documents for graduate-level applications include: a statement of purpose and research proposal, official academic transcripts, official graduation (or expected graduation) certificates, academic/employment history forms, recommendation letters, and identification documents such as a copy of your passport. Depending on where you live, you may also need residence-status documentation, and language scores (TOEFL/IELTS/TOEIC and/or Japanese competency evidence) may be required or used for exemptions.
Chaw Su Thin also described the MEXT-style flow in a very practical way: she said one of her first steps was to “contact a professor” to secure supervision, and she explained that she had to prepare documents for the university and then “prepare documents again” for the MEXT submission, so expect two layers of paperwork if you pursue a government scholarship route.