I've just done my first Japan checkin on Foursquare - it was non trivial. Firstly, I had to add a location via Foursquare's website. This was a real challenge as the site is not really aligned with the way in which Japanese addresses are expressed. After a lot of hacking (throughout which Foursquare kept telling me it couldn't find the location) I figured out that if I could tickle the Google location search via the Foursquare interaction, I could get the right place to show up. Finally, this succeeded and I added 京急富岡駅.
This would have been a lot easier if I could have directly located the venue on the map (as a lat/lon position) and then simply named it. That mode of entry seems like a pretty general backup plan for any problems, and easy to implement, so I'm assuming it is not available due to some potential for abuse.
Then I wanted to check in. This is can be done via the Foursquare mobile web page (first you need to update your location).