My employer just sent me an email detailing how much residence tax I need to pay before leaving Japan. And it is humongous. If I am leaving say on or before 20th June (can be adjusted), how much tax I need to pay?
My yearly income ~ 5.4 million yen
P.S. I have been living here for around 5.5 years
You should pay all of it. As a new resident, you get all the benefits without paying a single yen for the first year - municipal tax comes in from your second year. The tax you’re being billed now is on the money you earned last year. You could theoretically skip out without paying it, but it might cause issues when you return to Japan, and you would be one of “those” foreigners. The exact amount is determined by your tax return for last year. If you didn’t have many deductions (like dependents, pension plan etc.) then your municipal tax might be quite high.
@CheapoGreg Thanks for your quick answer! 
How is the municipal tax calculated, may I ask?
As far as I know, if I am in Japan on 1st of Jan of a year, I am required to pay the whole year’s tax i.e from Jan to Dec.
And considering it is 6% of my salary so it should be around 324,000 yen
When I am looking at my pay slips, I see from Jan to April there is deduction for Jyumenzei of 19,900 Yen every month. (i.e the tax is divided throughout the year)
So that would require me to pay around (3,24,000 - 19,900x4) = 244,400
The email mentions payable tax to be 331,200
The breakdown that they gave me, 331,200 = 19,900 (for May since I am leaving in June) + 311,300 (for next year)
So I am wondering did they calculate the residence tax for next year from this June to next year’s May?
Sorry for the confusion, but I am still so puzzled with the calculations…
Any help would be greatly appreciated!
P.S Not trying to skip it because I am expecting my lumpsum pension (kosei nenkin) to arrive when I return to my home country 
@CheapoGreg
I am pasting the exact japanese sentence that was in the email. Again thanks for your help! I really appreciate it!
5月給与にて来年度分住民税（311,300円）も徴収
住民税内訳（2020.5月分：19,900円＋来年度分：311,300円＝331,200円）
Wait! Don’t you have to work 25 years in Japan in order to be eligible for Kosei Nenkin?
They have changed that requirement to 10 years now.
And in my case, it’s less than ten years, so in such a case you can ask for lump sum pension withdrawal. The only thing is you will get about only 3 years worth of pension if you ask for lump sum withdrawal, even if you, lets say, stayed here for 9 years or so
Thanks for your reply Adam,
I arrived in 1980. You guys have it 100 times easier than we did. The crap we used to take. Anyways,
Thanks
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Hello! Could you please share what you ended up doing?
I will be leaving Japan in April 2021, and I am wondering if I have to pay residence tax for income received between January 2021 and April 2021?
I am aware that I have to settle the residence tax from my 2020 income, but I am wondering if I have to also pay for 2021 since I wont be a resident on January 2022.
Thank you in advance!
Yeah, you need to pay the tax for Jan 2021 - April 2021, to be more precise May 2020 - April 2021 (fiscal year)
How it works is like this, when you arrive in japan the first year you don’t need to pay residence tax and they say it’s free. But that’s not entirely correct, you pay the tax at the end of the fiscal year.
So if you come and leave within that one year, then yes you don’t pay any residence tax and it is indeed free. But if you stay more than one year, you pay the tax of the first year at the end of the fiscal year.
In conclusion, April/May is the right break-even point to leave Japan since you pay for the time you have resided essentially.
Does that make sense?
Thank you for your quick reply 
I see. I was hoping that since I won’t be a resident on January 1st 2022, that I won’t be required to pay the residence tax.
Hi, I would like to know more about the resident taxes before we left Japan. What will happen if we forgot to pay for it? For example, if one day we need to return to Japan and apply for the new visa. Would they still allow us to apply the visa and then ask to pay later when we arrive?
Also, about lump sum, is that any guarantee that if we safely received our lump sum means that we paid the last resident taxes when we left Japan?