If you live in Japan under a status which allows you to work and make money, you almost have to pay residence taxes along with your social security premiums.
If you are employed, your residence taxes are deducted before you get paid in most cases. This is special payment or 特別徴収.
On the other hand, if you work part time or self-employed, you must pay your residence taxes by yourself. This is ordinary payment or 普通徴収.
It is strongly recommended that you keep all the receipts of your residence tax payments especially if you are interested in applying for permanent residency in the future.
The Immigration Bureau needs to make sure whether your residence taxes have been all paid on or before their due dates. As long as your residence taxes are deducted by your employer, the Immigration Bureau does not demand evidence of your payment on or before the due date, but you must prove that your residence taxes have been paid on or before the due date if you pay these by yourself. The only credible evidence will be their receipts or bank records with specific dates.
Local governments issue Citizen Tax Payment Certificate Related to Delinquent Tax Proceedings, but this does not persuade the Immigration Bureau. If you refuse to pay residence taxes, the local government will eventually confiscate your property, and they will issue a warning beforehand. However, the local government does not issue such a warning if your residence tax is not paid a day after its due date. For example, if your residence tax is due on Monday March 31, and you pay Tuesday April 1, the local government does not issue the warning. Consequently, Citizen Tax Payment Certificate Related to Delinquent Tax Proceedings will prove that you have paid all your residence taxes “on time.”
However, the Immigration Bureau demands that all your residence taxes be paid truly on or before the due date. Consequently, you must submit either your receipts or bank records as evidence if you covet permanent residency.
If you are self-employed in Japan for 10 years and apply for permanent residency. you must keep every single receipt of your residence tax payments, but this is the requirement. I strongly urge you to keep these for your future’s sake.