I made an application for a postgraduate MEXT scholarship last year via the Japanese embassy in London. I've already forgotten a lot of the process but I'll share what I can remember. Blogs like these were helpful for me when I applied so it might benefit somebody else out there too.
I won't go over all the details of the application requirements and timings etc as there's already a lot of info available, but I'll try to give a quick review of my experience.
I started preparing several months in advance. I wanted to study on a masters program in a chemistry related field. I hammered out a fairly specific idea of what my thesis would be and then searched for suitable programs in Japan. After a lot of online research I narrowed down 4 or 5 options. I was actually living in Japan at the time so I visited two open days of the programs I was interested in.
After meeting a couple of potential supervisors in person and discussing the research they were carrying out I chose my first choice university and wrote a detailed and researched thesis proposal. The problem I encountered at this stage was writing a proposal that would be flexible enough to be submitted to three different departments with slightly differing research programs.
I was lucky that the professors at my first choice university seemed interested in me and my proposed research. They were very receptive to my emails and even invited me to attend a seminar and visit their laboratory, which I did.
Unfortunately I had real difficulty contacting potential supervisors at the other universities. It seems that many universities are not on the ball when it comes to updating their websites. After several weeks of trying to contact staff members via telephone and email, I was told that one of them had retired the previous year (they hadn't removed his research program from their website) and another had decided he didn't want to accept any more foreign student on his program (again their website stated otherwise).
Anyway, I made my application to the embassy, and a few weeks later I received an invitation to an interview. In terms of the application, I would say you need to have a clear, detailed and well written proposal. I spent several months researching and preparing mine. I included a reading list and a full reference list with citations. I included a gantt chart to show a time line for my research. I also sent my proposal to friends with postgraduate experience, so they could give me feedback. I researched the relevant industries in Japan and the UK and tried to explain why Japan was a suitable place to do my research and how I could apply what I had learned back in the UK. I discussed specific examples of Japan's role in shaping the industry in the past and how I might be able to use my experience in the future.
I don't know exactly how your application is judged, but I worked on the basis that they're looking for someone to make an investment in, who will be able to build industry/academic relations between Japan and their home country. I have no idea if that's why my initial application was successful, but I'd say it's probably a good way to think while preparing your application. If they spend thousands of pounds on sending you to university, what are they going to get in return?
The interview:
It goes without saying, but arrive on time and dress formally. There were about five of us there when I arrived. I got the impression they staggered the interviews and saw about 10 people a day (that's guess work). I arrived quite early and my interview stared about 20 minutes early.
Based on what I'd read online about other people's experiences I'd prepared myself for a not too difficult interview, but I was expecting questions about my research and the opportunity to talk about my future goals. I think in the email they told me the interview would take about 30 minutes so I was prepared to go into some detail and try to explain my research.
The interview was not what I was expecting. The gentlemen who interviewed me were very friendly and polite and I felt at ease right away. But frankly they seemed uninterested in my research. Obviously they're not scientists so I didn't expect them to ask in depth questions, but I got the impression they had skimmed my proposal a few minutes before I walked in. They asked me one or two very generic questions each (Why this university? What do you think you will do after you graduate? Etc.), and a few questions about my time in Japan. I tried my best to really give them some detail and explain the benefits of my research, but I got the impression they were not interested, and they quickly seemed to run out of things to ask me and ended the interview after about 10 minutes. I could think of about 10 good questions they could have asked me in the extra time, so I felt like an opportunity had been wasted. Maybe I'm just exceptionally boring and they didn't want to talk to me…
You've probably guessed I didn't get any further, which is fair enough, there were probably just candidates there who were better. I'm sure the interview experience varies greatly with location and from year to year. I suppose based on my experience, my advice is be prepared to steer the conversation and, though I hate to say it, sex up your research and make it sound exciting and interesting as well as worthwhile. I assumed they wanted to hear an academic style and detailed proposal, but they probably have to sit through dozens of those in a week or two, so maybe the ones that stand out are the ones that are more exciting. Good luck with that if like me your research sounds very dull to the layman! I was also planning to ask some questions in the interview (it's usually a good opportunity to make a good impression), but was not invited to, which seems very odd to me.
There's also the Japanese exam. Most people in my sitting left immediately (presumably they didn't know any Japanese). If you do speak Japanese, you can choose the level of the test. I forget if there were two of three levels. The first level, which I tried, is broadly similar to N5/N4. You need to be able to read hiragana and katakana and some kanji, and there's a writing section too.