http://www.japan-guide.com/forum/quereadisplay.html?0+6...I think your question got moved from the above thread, correct?
When they say you need Alien Registration Card, what they mean is that they need to see that you have an address in Japan (not just staying at a hotel, but at an address you live at).
So if you moved to Japan, and find a house/apartment to stay in (I assume you are going to be staying in Japan long-term if you are establishing a company?), then you can go ahead and register for the ARC at the city hall of the city where you live.