Your situation is quite strange. Normally, MEXT scholars come to Japan as research students, and after 6 months or more (no longer than 2 years), they will take entrance examination to enroll master or doctoral courses officially. Therefore, you do not need to take entrance exam when you are applying for MEXT. After you pass first round, you will receive a certificate from your embassy, and send it together with other documents to your university to get letter of acceptance. I think you should contact your university to avoid misunderstanding.