There are two ways: 1. Apply through Japanese Embassy, appear in a test and get selected (depends on your academic strength though). 2. Directly write to the professor of your choice, request him/her to apply to University for your scholarship (Monbukagakusho). Both schemes would award you 180,000Yen/month (tax-free & tuition-waived). It may take a year to process and get approval. There are some universities which have special program for Master and PhD courses (Hokkaido University: contact HUNSA for detail) Goodluck with your higher study.