Can I apply COE and Visa with different passports?

[dakenko]

I hold dual citizenship for Country A and Country B. I've obtained my Certificate of Eligibility (COE) for Japan using my Country A passport. Can I apply for a visa in Country B using my Country B passport https://speedtest.vet/https://vidmate.bid/ ?

Apologies I can't reveal the countries due to security reasons but I would really appreciate some guidance on this. Thank you in advance