Multi-Entry with 12-month Validity application for permanent resident Australia national

Hi, I would like to apply for the Multi-Entry with 12-month Validity Visa for frequent business travel between Japan and China, and I would like to clarify where I should submit my application. The information above seems to indicate that I should apply via a travel agent, is this correct even for the multi-entry one? If possible I would like to apply for it before booking my flights, which would be difficult to do via a travel agency. Is there the option of submitting my application directly to the embassy in this case?

I am a permanent resident in Japan.

Many thanks.