travel agency is an obligation for nonjapanese?

Hi! I'm Ecuadorian but living in Japan (I'm exchange student) and I want to visit China in august so, is there any way I apply for the visa at the embassy directly? Or I MUST do it through a travel agency? They're charging me ￥16500 for one entry which I think it is too much so I guess if I skip the travel agency would be cheaper. Can I do that?