Honduran in Japan going to China for a 3 months training program

Hello, I'm a Honduran citizen, I am currently in Japan for tourism and I got an 3 months internship opportunity with a foreign company in Beijing. Currently there's no Chinese embassy in my home country so I have to do all the process in a third country. I have all the documents in order, which includes an invitation letter from the sponsoring company, details of my stay, flight schedule, hotel reservations, traveler's insurance, valid passport with temporary visitor permit to stay in Japan, etc. Can I do the process while in Tokyo?