You need to prepare a research proposal, write a test and appear in an interview to first earn the scholarship nomination (it is just nomination not a confirmation) at your local Japanese embassy.
You need to get a tentative acceptance by at least one professor at a Japanese university in the form of a "Letter of Acceptance", in a particular format (provided to you by your local Japanese embassy once more).
You need to give this Letter to your local Japanese embassy so they can get a confirmation from MEXT in Japan that you will be joining that univ and that particular prof as a research student, a noteworthy point here is that they can put you in some other univ. Then you go to Japan and learn Japanese for like six months and side by side prepare for entrance test to the "actual Phd program". Till this time you will be just a research student who wont get any type of degree or certificate...
Once and if you get admission as a regular Phd student, you will need to "extend" your scholarship which means another test and interview with MEXT and a letter of recommendation by your prof. Here there is a HUGE Risk.... as unlike masters, it happens quite often that you may have every other thing leaving the scholarship... you may try to get another scholarship there are quite a few of them, or if you are lucky your prof may support you out of his research fund, though it is unlikely... as one reason MEXT scholarship candidates preferred over others by Japanese profs is due to the fact that they dont require funding for tution etc...
So you then work on your Phd... it takes usually 3 years + 6-10 months of research student period...
Not to mention you need to start 1 year ahead for getting the scholarship in the first place...