If you live in Japan and apply for a residence permit for study or research or for a work permit for more than 90 days in Sweden must show your passport to the Swedish embassy in Tokyo in person before the Swedish Migration Agency can make a decision. Just like previously, this application is to be submitted online.
You will be contacted by the Swedish Migration Agency or the Swedish embassy in Tokyo if your passport needs to be checked. Therefore, you cannot visit the embassy before being contacted about it.
If you have any co-applicants such as your family members, they will have to show their passports as well as you do. Children under the age of 5 are however exempted from that.
If you once applied for a residence permit in the past and showed the same passport at that time, you will not be requested to show it again.