Living at Australia, how can I buy iPhone SE (japan version) from Apple Store?

Australia and Japan get the same iPhone model. Model A2296 (GSM/CDMA): https://www.apple.com/iphone/LTE/#iphone-se

So buying in Australia essentially gets you the same model as the one sold in Japan.

Why do you need the Japanese model exactly?

You can't. You can buy the Australian version from the Australian store.

The only way to buy the Japanese version short of going to a store in Japan is if you have a Japanese credit card, and shipping address. Apple will not ship the device to another country.