Applying at Chinese Embassy or through travel agency?

I am Swiss, my girlfriend is Polish and we need to apply for a chinese Visa in Tokyo. I am reading mixed information whether this needs to happen through a travel agency or if we can go directly to the embassy. Apparently it needed to go through a travel agency, then changed in Sep 2013 and now I have read in a forum it changed again very recently. Does anyone have the latest information? If it does have to go through an agency, what agency is recommended? Thanks!