Yeah if two universities nominate you to MEXT at the same time, you will be disqualified. That's why I learned from my advisor when applying to MEXT through Titech. So be careful with your choice.
thank you very much for your information! it's so lucky that i post to ask here. otherwise i would mail two applications!
btw, the two offers i've got are Keio U and U Tokyo. I am so afraid of failing in getting scholarship. which one do you think will have a higher chance?