Congratulations
Generally speaking once your university recommend you for the MEXT scholarship, you will be accepted by MEXT. It's just a matter of paperwork because MEXT has set aside a specified number of scholarships for each Japanese university which the Japanese universities have already applied for. (they apply to MEXT for a certain number of scholarship slots, and are accepted or rejected based upon their plan for how to use these scholarship slots. These days MEXT Is a little bit more severe/strict on the Japanese universities, and the scholarships are less common or fewer in number than before, but once you were recommended by your Japanese host university that means that they are using one of their alloted slots for you and it should be a matter of just MEXT receiving the documents and approving themBut the universe he will not tell you that you are approved until all the documents have been officially approved. But sometimes professors will tell you unofficially that you should get the scholarship it depends on the professor.
So for all intensive purposes you should be OK.
I hope that helps