You should have a Carnet to enter Japan. It is VERY difficult to bring a vehicle to Japan without a carnet, so I only give information on entry with a carnet.
Your carnet must first be "authenticated" by the Japan Automobile Federation (JAF). The phone number of the International Relations Division is 81-3-3578-4910 Fax number is 81-3-3578-4911 (Change 81 to 0 when calling from inside Japan). They do not have a public E-mail address.
1. Fax your Carnet to JAF before you arrive.
2. Take the original Carnet to JAF.
Verification only takes about 10 minutes if you contact JAF in advance. They will have all the paperwork ready. It will take longer if you just show up at the office.
Ask for a Japanese language copy of the laws on foreign vehicles in Japan. A copy is available here (in Japanese) if you don't get a copy from JAF. It is helpful if the police stop you because most police officers don't know you can legally drive a foreign bike!
You must have third-party insurance in Japan. You can get this at any motorcycle shop. The minimum coverage is one month. Mandatory insurance is called “Jibaiseki Hoken,” and it only covers for personal injury and death of the other person in an accident. Print out this form and show it at the motorcycle shop.