Here is more information about lowering your taxes.
You made a donation to national government, prefectures, municipalities, or specific non-profit organisations? Then you may get a benefit through your tax return.
Recently, Furusato-tax (donations to municipalities or prefectures) is one of the most popular donations. What is Furusato-tax? Furusato literally means 'Hometown', so it sounds like people make donations to their hometown. But actually it does not have to be their hometown (and it is ok if your are foreigners), and people can choose any municipalities or prefectures they want to support. Through this support, donors can receive some local gifts (e.g. beef, vegetables, etc.) from municipalities or prefectures. What you will receive depends on which municialities or prefectures you choose to support (you will see before donations). Also, donors get tax benefits. So great thing is that local gifts and the tax benefit will almost offset your donations.
You can visit the website below.
(seems Japanese language only)
Japan is one of the most earthquake-prone countries so you need to be ready for that. Many Japanese people pay earthquake insurance premiums for their properties. You get a tax benefit from this payment. At most, JPY 50,000 would be deducted from your annual income. If you are an employee, you just give a receipt to your company to get this benefit. But some cases, you need to do a tax return.