You can report your Japanese pension income under Wages & Income > Miscellaneous Income, 1099-A, 1099-C > Other Reportable Income > Other Taxable Income.
Enter 'Japanese Pension' and Amount. The income will show on Schedule 1, Line 8z and be carried over to Form 1040.
In the Foreign Tax Credit section, you are first asked about 1099-Div, 1099-Int. Continue through the screens until asked if you have other Foreign Income/Tax to report. Choose 'General Income' from the income types, and enter the amount of your pension. This is not double taxing; it is to tie it into the tax you enter on a later screen.
Continue and you will be asked to enter the Foreign Tax you paid on this income. Continue to the end of the section.
This will create a Form 1116 in your return, for a Foreign Tax Credit.
Here's more info on Claiming the Foreign Tax Credit.
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