Customs

Two questions get asked at the same counter and answered by different rules: how much duty do I owe on this, and may this enter Japan at all. They are worth keeping apart.

QuestionGoverned byWhat "no" costs you
Is it inside the allowance? The duty-free allowance for travelers You declare it and pay duty. Routine
May it enter Japan? Quarantine, health and customs law The item is surrendered or destroyed, and a false declaration is an offense

Being over the allowance is an ordinary transaction. Bringing something inadmissible is not, and the two have nothing to do with each other: a ¥3,000 sausage is well inside every allowance and still cannot enter.

And it is not the shop kind of tax-free

"Tax-free" on a shop window is consumption tax on goods you buy in Japan, refunded when you leave. It is a different tax, decided by a different authority, and it does not touch the allowance you spent on arrival. That one is here.