We use it online.You can pay tax throughout the year, but you can only deduct the tax in the next year (if you use Furusato this year, you can declare it on your tax return next year). You will receive a receipt from the local government, which you will use to file your tax return. I believe the declaration can be done at the tax office😀

I found a website which is available in English. I hope this will be helpful to you.

https://www.furusato-japan.com/furusato-nosei-info/about-hometown-tax-scheme