What should I do in this situation?

Last August in Outlet Park in Chiba, a shop tax exempt the items I have bought, and taped the receipts in the passport, so I thought that I am eligible for tax free shops. Last Saturday we came to the same outlet shop again and surprised that they wont give my companion tax exemption for the things he bought. The personel in the cashier explains that we are ineligible for tax exempt because the duration in the visa is 1 year (visa type: intra company transferee). We show him the tax exempt receipts in my passport, and they said that its a mistake of the cashier personel at the time. We said to them that maybe when leaving the country it will be a problem. What should we do

I'd say visit your local tax office and explain; hopefully they'll just make you pay the tax you haven't paid.

You are not eligible for tax free buying if you are not a temp visitor. One year visa is not a temp visitor.