I applied in the Graduate School of Informatics (a non special programme; yes there are 2 types of programmes). I applied in January (around 20th). I got approved by the University by 10th of February. And got my confirmation last week.
This is the result for my college Application Procedures for Master's Programme | East Asia Sustainable Economic Development Studies
I got the letter of acceptance by the Uni by 14th Feb. And now im waiting for the final result from Mext.