I don't know what you mean by being recommended by your embassy. Is that a requirement for Turkish students to study abroad? Or is it a requirement of Japanese universities of Turkish students?
To apply to universities here in Japan, go to their web sites and see what they want you to do. There are probably differences in each one.
You can't lose a scholarship like that. You get a scholarship to attend a specific university, I think. Ask the scholarship agency.
Don't you have a university study abroad counselor or department that can answer all of these very basic questions?