Individual Tax Calculations

Hi everyone! Hoping I can get some tax questions answered because my company is hopeless (Foreign company with no local HR/Finance function 🙁 )

I got to Japan last November. The company wanted me to start work ASAP and I had a working holiday Visa, so basically I started my full time job on my working holiday visa. I started the job in late November.
We are working on getting a Work visa now (likely to be issued in about 2 months time). I am definitely here in Japan to live and work indefinitely and my job is also ongoing.

I must admit, all my payslips were in Japanese, so I didn’t really look to much into it- but I did today because my pay was significantly lower than the previous month. And I found out I got taxed at around 45% this month (compared to \~20% last month).
I know my Dependents Declaration form was missing- which I submitted now- just wanted to check if that would fix the tax rate moving forward. And how the overpaid tax is adjusted- is it normally throughout the year, or at the end of the year through a tax return?
It’ll be easily 2 months until I hear back from my company’s HR, and I would love to get some reassurance on this 🙁
Also, I thought the Income Tax for 2024 would be based on my 2023 pay (which is really not much, as I only worked 1 month).
Is the 20% tax rate because of my Working Holiday Visa?
When I get my work visa finally issued in May, does that mean that my tax withheld up until May will also be adjusted to a resident rate? (Or will it be non-resident rate until May, resident rate after May)?

I did some searches and there was a comment from u/starkimpossibility that ” If you can demonstrate that you have very strong prospects and intentions of living in Japan longer-term, you could make the case that you are a Japanese tax resident and should be taxed accordingly”.
I’m sure my company will vouch for this from beginning of my employment last November. So I’m hoping all the taxes I’ve already paid can be adjusted….

I’m legit flying solo here, so would appreciate all help!!!

Thank you so much!!

by echon10

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