According to a Nintendo of Japan customer service representative, the 3DS will be region-locked. This means that if you import a Japanese system and attempt to play a North American game, it simply will not work.
As disappointing as the news is, I don’t think this should be a big surprise to anyone. After the DSi implemented region locking, there really was no going back. Nintendo has yet to officially comment on the issue, but I’d say this rumor is very likely.