In principle, an application for issuance of a certificate of eligibility should be filed at a regional bureau or a branch that has the jurisdiction over the location of the organization accepting the foreign national or the domicile of his/her relative who will serve as his/her agent, or at a regional immigration bureau that has the jurisdiction over the location of the organization accepting the foreign national or the domicile of his/her relative who will serve as his/her agent.
(source: Immigration Services Agency of Japan)
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