Submitting your new site to good quality directories is certainly one of the first tasks most link builders would handle. When you post to the right places, you can get a bunch of fairly relevant backlinks, some of which carrying decent authority. That’s a fine way to start an SEO campaign.
If you think of the English webosphere, you have a good number of these directories (at the very least a few dozens of good quality ones), and submitting to them all will take you quite some time.
Thinking of Japan, your options are more limited… you can litterally count the big players on a Simpson’s hand:
-Yahoo!: just like in the US, it will cost you an arm and a lung to submit there, but it’s the strongest one, by far.
-Dmoz: where patience is a virtue. I hardly see any changes on this directory anymore, but, it still carries quite some weight in search engines, so… give it a try anyway.
-Rakuten: They have a directory which looks a lot like Yahoo’s except it’s free. What’s more, the last time I checked it, it was autoapprove, as long as you registered on their site.
-Your local Chamber of Commerce: if you have a business ID in Japan, you are eligible for a free listing, including a backlink, on your local Chamber of Commerce homepage. Just Google it!
Besides these websites, there are maybe a handful of sort-of-decent directories. Business listings, local listings, these kinds of directories that focus on a area or speciality. But once again, it may take time until you find one that has decent contents and doesn’t require you to link back.
Long story short: don’t spend too much time looking for and submitting to directories for your Japanese page, get a few acceptable links to give your site a kick-start and focus on more important things.