When you buy a car, before you can actually receive it you must have a police-approved parking space within 2km of your house. That is, unless you live in a tiny village with low population density, in which case the process is much simpler (though I can't offer advice as of yet).
You can pay your car dealer to do all of this for you, although I was quoted 30,000yen which seemed like too much. To do it yourself, follow these steps:
(UPDATE 9/2013: Details about the specific forms used in this process can be found here.)