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The Working Holiday visa application should be submitted electronically to the Swedish Migration Agency via their website.
More information and application website here.
After the decision is made;
The decision paper will be sent to the embassy or consulate-general you selected in your online application. If you select the embassy in Tokyo, the embassy will send it to your address in Japan by post. So, you do not need to visit the embassy to receive the decision.
If your application is granted, you will travel to Sweden only with your passport and the decision paper and show both at the border control on arrival. After arriving in the country, you must book an appointment with the Migration Agency to have your fingerprints and photograph taken for being issued a residence permit card.
Sweden has diplomatic relations with almost all States in the world. It has embassies and consulates in around half of these. Sweden's foreign representation consists of approximately 100 missions abroad and 350 honorary consulates.