You mean the trading card game right?
Only 2 places I've seen carry them-
www.amazon.co.jp and
www.animaxis.com
I believe both are all out of stock (the last booster pack was released, eh, almost a whole year ago? in spring 03)
At amazonJP you'd have to search for fullmetalpanic in katakana, or search for each set's ISBN # (available on the FMP site stuff info page)
Alternatives-
*auctions.yahoo.co.jp - they used to show up here (been a long while since I cruised there). You'd have to learn about proxy bidding via someone like Rinkya, Celga, or Anime Chaos (no urls, try googling). They are pretty pricy- bidding services aimed at cel collectors.
*ebay.com - I've seen someone auctioning simple card lots every now and then. Not too many looking for these cards so they should be cheap that way, if you're lucky and there's an auction up when you look. If you're registered, you used to be able to set a search term and have ebay email you whenever a matching auction was listed.
I don't think they do this anymore though
*try finding a private seller via an anime trading card group- there's an active group over in groups.yahoo.com. I know from personal experience that anybody trying to collect most of these regular cards will have tons of extras.
**I have alot of cards, but I'm not ready to do anything with em yet. They need a good sorting, but once I do that I'll be looking to offload the extras somehow.
Good luck, and please post if you find anywhere selling packs or boxes