Starting position
— coe
You married abroad and have not reported it to Japan yet
You held the wedding and completed the paperwork in the foreign spouse's country, and nothing has been filed on the Japanese side.
Until the marriage is reported to Japan, it does not appear on the family register — and the 戸籍謄本 is what proves the marriage to immigration. The visa application cannot usefully start before that.
The report can be made at a Japanese embassy or consulate abroad, or at a municipal office in Japan. You will need the foreign marriage certificate with a Japanese translation naming the translator.
The order things happen in
-
Report the marriage to Japan
At a Japanese embassy or consulate, or a municipal office. Bring the foreign marriage certificate and a Japanese translation. -
Wait for the entry to appear, then obtain the family register copy
A report made abroad takes longer to reach the register than one filed in Japan. -
Proceed as for a normal Certificate of Eligibility application
Your foreign marriage certificate is also submitted, so keep the original.
Watch out:
If your own country will not issue a marriage certificate because the marriage was registered in Japan first, the Agency's Q&A says to submit a written explanation of the circumstances in its place. Name the authority you approached and what they told you.
Starts on the coe route, so you are only asked the questions that apply to this situation.
Sources
Family register Q&A on international marriage and birth abroad
法務省民事局 / MOJ Civil Affairs Bureau
Immigration and residence examination Q&A
出入国在留管理庁 / Immigration Services Agency
Status of Residence "Spouse or Child of Japanese National" (applicant is the spouse)
出入国在留管理庁 / Immigration Services Agency