Yes, because there is only one tax authority (国税庁, Kokuzeichou, National Tax Agency).
Here in the US, we have more than one tax authority:
We have the IRS, which is the federal tax authority.
Each state then has their own tax authority.
Each county then has their own tax authority.
Each city then might have their own tax authority.
And we must submit filings and returns with and pay taxes to all of them as applicable, and they all operate on their own laws, regulations, and taxes.
To reframe this, let's talk about sales tax. In Japan, there is only one nationwide sales tax; because there is only one tax authority.
In the US, sales tax might be levied at the state, county, and city levels as applicable (federal doesn't levy sales tax, as far as I'm aware). Some might not have sales tax, others might, and they are all different rates. The sale tax in one city will be different from its neighbouring city.
TL;DR: Paying taxes in the US is complicated because everyone wants their taxes.