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日本政府发放奖学金的方法，一种是通过日本驻外使馆向国内文部省推荐；另一种方法是通过日本国内的大学向文部省推荐。一般一年中有两次申请机会，入学时间分别是每年的4月1日和10月1日。
通过大使馆申请的学生，需要到使馆申请表格，并通过文部省的选拔考试。通过日本国内的大学向文部省推荐，这是大家比较多见的一种申请方式。就是文部省每年对日本国内的大学都会分配一些国费的名额，主要针对国立大学，一般来说越好的学校分配的名额越多。通过日本国内的大学向文部省推荐这种申请方式，需要申请人在我国就读的大学跟日本学校签订一个合作交流协议，一般需要两个学校的院系领导签字。在有了交流协议的前提下，申请人可以开始在联系导师的指导下，填写文部省奖学金的申请表，准备申请材料。申请材料内容比较多，有10多项。例如，对于申请博士后期课程的申请人需要提交下列材料：
(1) Application Form.
(2) Application for Japanese Government (Monbukagakusho) Scholarship (PDF).
(3) Certificate of health (PDF) issued within the last 2 months.
(4) A copy of an official document to indicate the applicant's nationality. (This can be replaced by a photocopy of the applicant's passport.)
(5) Certificates of Bachelor's and Master's Degrees (or their equivalent).
(6) Official academic records from undergraduate and graduate courses.
(7) Recommendation letter addressed to the president of Kyoto University written by the dean of the applicant's graduate school
(8) Recommendation letter written by the applicant's supervisor at the graduate level.
(9) Recommendation letter written by the applicant's supervisor at the undergraduate level .
(10) Recommendation letter written by the head of the applicant's employing organization (if the applicant is currently working.)
(11) Research plan at Kyoto University (A4 size, 3 pages).
(1) Application Form.
(2) Application for Japanese Government (Monbukagakusho) Scholarship (PDF).
(3) Certificate of health (PDF) issued within the last 2 months.
(4) A copy of an official document to indicate the applicant's nationality. (This can be replaced by a photocopy of the applicant's passport.)
(5) Certificates of Bachelor's and Master's Degrees (or their equivalent).
(6) Official academic records from undergraduate and graduate courses.
(7) Recommendation letter addressed to the president of Kyoto University written by the dean of the applicant's graduate school
(8) Recommendation letter written by the applicant's supervisor at the graduate level.
(9) Recommendation letter written by the applicant's supervisor at the undergraduate level .
(10) Recommendation letter written by the head of the applicant's employing organization (if the applicant is currently working.)
(11) Research plan at Kyoto University (A4 size, 3 pages).
(12) List of scientific publications.
(13) Brief description of academic achievements (A4 size, 3 pages).
(14) A copy of Master's Thesis (or equivalent).
(15) A copy of an official score of TOEFL taken within the last 12 months unless his/her mother tongue is English.
注：根据各个学校不同，提交材料或许会有较小差异。申请10月入学的材料，最晚要在1月底或者2月初交到学校。然后就是申请人的第一次选拔，也就是学校选拔。各个学校根据所有申请人的情况进行排名，挑选出排名靠前的，报送文部省。这个过程在3月结束，申请人会收到学校的结果通知。文部省审批是一个漫长的过程，要等待几个月的时间，一般6月底或者7月初申请人才会收到文部省结果通知。一般来说，通过了学校选拔的申请着，获得文部省奖学金的希望是非常大的。
