Australian/South African dual citizen

I have a pretty complicated issue, and every embassy/consulate I ask tells me to ask someone else...
I am a dual citizen of South Africa and Australia. I came to Japan on my South African passport 3 years ago, and my latest working visa is going to expire in 2 months. I have just lost my job and I'm having a lot of trouble finding a full-time job with visa support. I'm not confident that I'll find one before my visa expires. I was planning to move to Australia with my Japanese boyfriend, but his father has fallen ill so he can't leave yet.

I am now faced with a couple of options:
(1) leave as a South African and come in as an Australian with a landing visa for 90 days and continue looking for work
(2) get a spousal visa by getting married

Neither of these options are very desirable. (1) Looks very suspicious to the immigration authorities, and if I do (2) on my South African passport then it'll be difficult to emigrate to Australia together in the future.

So, I want to know if it's possible to change my current status of residence (working visa) over to my Australian passport. Also, any other ideas for how to stay in Japan would be welcome!

(1) Looks very suspicious to the immigration authorities, and if I do (2) on my South African passport then it'll be difficult to emigrate to Australia together in the future.

I don't think that (1) would be very suspicious. It is not unlikely that immigration cannot match your "South African identity" with your Australian one, and that you will be treated as a "new person". Even if they match your passports/fingerprints, you have nothing to hide. After all, you have two passports and have not done anything illegal, I assume.

And I do not see why (2) would make emigration to Australia difficult, as marriage and passports are not interrelated.

However, if you think that changing your current status to your Australian passport would solve your problem, then I recommend to inquire at your closest immigration bureau. I have the feeling that it should be possible.

How fortunate you are 'dual citizen'. You can go to South Korea and turn-around for Japan and enter relying on the Australian passport as a tourist.... If you elect to go to Ausralia enter using the Australian passport (enter/exit) to eliminate immigrating to Australia.