It's not clear what you might mean about your 'IRA' unless you meant IRS. Under the US Internal Revenue Code, most foreign pensions are not considered a “qualified trust.” That makes them ineligible to be rolled over. Assuming you did not rollover your retirement distribution you will pay tax on the full amount and then receive credit.
As indicated by @ThomasM125 the credit will be based on the lesser of the US tax on the distribution or the tax paid to Japan, whichever is less.
Follow the steps in the link below to enter your foreign tax credit.
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