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National Tax

There are 6 ways to pay the national taxes.

Direct Payment

“Direct Payment” is available when you file tax return by electronic filing (e-Tax).
Even if you do not use the internet banking, you can instruct tax payment from e-Tax software. 
However, advance notification to the tax office is needed and it would take around one month after the notification until the direct payment becomes available. 
You can designate payment date.
If you authorize your tax accountant, he/she is able to instruct tax payment on behalf of you.
Besides, on or after January 4, 2019, you will be able to select a bank account for the tax payment from the multiple bank account provided that you have filed the advance notification for each of the bank accounts.   
The payment is made through a Japanese e-payment platform so called “Pay-easy”
It automatically produce set of information necessary for payment through Pay-easy such as “revenue authorities code”, “payment code”, “verification code”, “payment code”, “tax amount” based on e-Tax then notify those details to the payment agent such as bank.

Internet banking

Payment with the internet banking is available when you filed the tax return via e-Tax.
It is also based on Pay-easy as same to the direct payment.
The advance notification is not required but payment instruction can be done by only taxpayer with the internet banking.  

Credit card 

You can make payment with credit card from the dedicated website ” 国税クレジットカードお支払サイト” .
It will charge 76 yen per 10,000 yen tax payment.

At Convenience Stores

Tax payment slips with a QR code or a barcode is acceptable for payment at convenience stores.
However, payable amount should be 300,000 yen or less per one payment slip.
On or after January 4, 2019, you can convert your tax payment information into a QR code by yourself using special website within home page of the National Taxation Agency then make payment with the QR Code at convenience store.   
A tax accountant is also able to create the QR code for you then send it to you for tax payment at convenience stores in your neighbors.

Direct debit

It is available only when you submitted application form for payment by direct debit to the tax office. 
This payment method is available for only “personal income tax” and “consumption tax (for sole proprietor) “, therefore no corporate taxpayer can make tax payment by this method.

At banks

Payment at banks is acceptable for any kind of tax.
However, you have to use designated payment slips specifically designed for process at the Bank of Japan.
Accordingly, banks will not accept other payment slips.
Tax offices use dedicated printer and paper to create the payment slip the mail them to taxpayers.
Therefore any other cannot create the designated payment slip. 
Some tax software can prepare “image” of the national tax payment slip however it is just reference purpose so that you can fill out the actual payment slip.

Local Tax

Local tax is far behind the national tax in terms of electronic payment.
Although all of the prefectures and municipals have accepted e-filing (eLTAX) from corporate taxpayers, only the below 22 local governments accepted electronic payment (as of November 7, 2018). 

As for local tax of province other than the above, you have to make payment using payment slips at banks or convenience stores (CS accepts only payment slips with barcode).

Fortunately, banks accept local tax payment slip created by a taxpayer as long as its format is in line with the standard format.
So you can create the payment slip using spreadsheet or tax return software.

Currently nationwide common platform for electronic payment of the local taxes are being developed.
It is expected that more local governments will join the new platform once it goes live.

(Added May 8, 2020)
With the launch of the “Local Tax Common Tax Payment System” in October 2019, it is now possible to electronically pay taxes to local governments nationwide.
However, not all local taxes can be paid electronically.
The current tax items subject to electronic tax payment (as of May 8, 2020) are as follows.
For tax items that have not been electronically declared, you can only make expected payments or deemed payments.
Unfortunately, the final tax amount payment data is linked to the electronic tax filing data, so, unfortunately, the electronic payment is not available for the final tax amount when you file a paper-based tax return.

• Corporate prefectural tax
• Corporate business tax
• Special corporate business tax (local corporate special tax)
• Corporate municipal tax
• Business premises tax
• Individual resident tax (only withholdings from salary)

Please refer here for details (Sorry, only Japanese).

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Tax filing and payment would be hard to deal with for foreigners living in Japan.
Tax accountants can take care of their filing but tax payment should be done by taxpayers themselves.
So they would face difficulty to fill out the payment slip or communicate with bank clerks in Japanese.
I hope tax payment using the QR code will be great help for such taxpayers.