There are many kinds of scholarships that universities can recommend you to. MEXT actually is not a specific scholarship, Because MEXT offer several types of scholarships. Normally, universities have so many slots allotted to them, and so when they recommend someone for that scholarship they are usually accepted. The 280,000 and you talk about is the fee for the first semester.
Depending on the situation, your university may be asking you to pay, so that you are an enrolled and registered student, so you will then be eligible for a scholarship. This might not be what everyone calls a MEXT scholarship, but some other program that is funded by the ministry (MEXT). What everyone loosely refers to as The MEXT usually has a full tuition waiver point-to-point airfare and ¥144,000 per month support for the duration of the program.
Since the first semester has already started, I assume you're in Japan ( let your program starts in October ) The other thing you can do to delay payment is to request a 50% tuition waiver which all national universities are able to give based upon your income. If you apply for this, then your tuition will be delayed until probably the end of the term because they have to evaluate your application. However doing this may, depending on the regulations of your particular program and institution, make you a self paying student and therefore not eligible for the scholarship you're applying for. The best thing to do is to go to gakumu and ask.
This is actually my advice to you, the reason I'm giving some details or possible ideas is to show you that probably no one can answer your question correctly except for someone in the student office (gakumu).
Unfortunately sometimes many people share information based on their experience, and regardless of experience, the facts/realities may be different.
Best thing: ask the university.