Try following these steps (you can not pay with a credit card this way so you have to use something different like PayPal):
1.Tap iTunes Store, App Store, or iBooks Store.
2.At the bottom of the Featured page, tap Sign In.
If you're already signed in, skip to step 5.
3.Tap Use Existing Apple ID.
4.Enter your Apple ID and password. Tap OK.
5.Tap your Apple ID.
6.Tap View Apple ID or View Account.
7.Tap Country/Region.
8.Tap Change Country or Region.
9.Tap your new country. (Japan)
10.Tap Next.
11.Review the Terms and Conditions and Apple Privacy Policy.
12.Tap Agree if you agree to the terms and conditions.
13.In the prompt that appears, tap Agree.
14.Select a payment method and enter your payment information. (From another FAQ: "The trick part of this is when you have a credit card associated to your Apple ID. If you have no credit cards selected or added, the None option is readily available and you can breeze through the process without a problem. But if you have added a credit card and the None option doesn’t show up, you will need to add a valid credit card whose address matches the country you have selected.")
15.Enter your billing address and tap Next.
Afterwards follow step 6 from my own guide.