Visa for Japan for South Africans

With the Rugby world cup coming up next year and just to travel to Japan in general do you know if:

A travel agency can apply for a visa on your behalf or do you have to go apply for it personally at the Taipei office?

Thanks ^^,

Might want to strictly state Rugby world cup.
I would guess most travel agencies help get visa, just like they would for travel to Vietnam, etc. Just give them your passport in person and they do the rest.