Japan keeps getting easier to launch a fully owned subsidiary. I'm on my second, and the process couldn't be smoother.
Step 1: Choose your advisor. Assuming you're coming in from the outside, a disinterested third party is a really good idea (and necessary and cheap). The two basic types are law firms and accountants. They do similar work and have similar cost structures. I advise that your choice be guided by 1) will you need an
Step 2: Choose your structure. Basically, there is seldom a reason not to go for a KK structure. There are other options, but they seldom will save any time, and do occasionally have some constraints. Some background is available here, but it is a little out of date, for example KK's do *not* get limited to 4x initial capital for their total capitalization. http://www.japaninc.com/mgz_autumn_2006_incorporate
Step 3: Choose your internal structure. I see this as binary: if it is a truly independent operation that will grow as its own company, you'll want the full package (3 person board, 1 representative director, 1 external
Step 4: Pull the trigger. You'll need to determine your initial number of shares and price per share. I suggest letting your incorporator do this (see step 1...that is their job). 1 share for 10K JPY for example. Once that is done, there is an official company. There are other tasks of course which I will get into later, but once you pay your bill (and in doing so, purchase that share) you have a company. This whole process can get done in 3 weeks (1 to prep, 1 to file, 1 to get the approval from the government).