Two mechanisms stack together to make retirement payouts one of the lightest-taxed forms of income in Japan. First, a deduction tied to years of service comes off the top: ¥400,000 for every year up to 20 (with a guaranteed ¥800,000 floor even for very short tenure), then ¥700,000 for every year beyond that. Second, whatever survives that deduction gets cut in half before ordinary tax rates ever touch it, the halving rule.
That combination is why long tenure pays off so disproportionately at payout time. Someone with 30 years of service gets a ¥15,000,000 deduction before halving even applies, more than double the ¥6,000,000 a 15-year employee gets, because the per-year rate itself steps up after year 20. It's a deliberate design choice rewarding long-tenure employment, historically the norm at large Japanese employers.
Resident tax on a retirement payout also behaves differently from ordinary salary. Rather than lagging a full year the way resident tax on your regular pay does, it's a flat 10% withheld immediately at the time of payout, calculated on the same halved taxable figure, with no per-capita levy attached. Submit the notification form to your employer beforehand and this correct, final withholding happens automatically, skip it and you'll face a higher flat withholding rate with a return to file afterward to claim the difference back.