Assuming you are an American or some other Western foreigner living in Japan with a re-entry permit, I think you need to fill out one of those disembarkation cards (available at the airport) before you go through immigration on the way out - then they will take half of the form from you on your way out and staple the other half to your passport. On the way back in to Japan (after your trip), you fill in your flight info on the half they stapled to your passport and sign it saying you aren't bringing illegal things into Japan and they take that from you.
Also, on the way back in at Narita (if you are going through Narita) you can go to the special line for people with re-entry permits - it saves a lot of time over waiting in line with the rest of the foreigners.
Don't take this advice as 100% accurate, but that's what I think will happen.
