Apply for Hongkong and Macau Visa at the same time from Japan

Hello, I have working visa in Japan, with Vietnamese passport. I want to visit Hong Kong and Macao at the same period. So can I apply for Hong Kong and Macao entry permit at the same time in Chinese Embassy in Tokyo, I mean do I need to use my passport to apply for Hong Kong entry permit first, then take my passport to apply for Macao's later?
Or I can do both applications at the same time at the Embassy?

Thank you very much.
Best regards,