You should apply separately in your respective places of residence. As @phoog comments, if you apply in India there’s a good chance that the application will be rejected with instructions to apply in Japan, because applicants are generally required to apply in their place of residence.
Since you are the primary applicant, and your girlfriend’s application is dependent on yours, you should apply first and your girlfriend afterwards once you have received your visa. You will need to provide her with your financial documents to be submitted alongside her own but there’s no need for her to do the same for your application.
Credit:stackoverflow.com‘
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