Certificate of Eligibility
 

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You do not need to send any originals. Just forward copies (scans are you best option). However, if they require a document to be translated into Japanese, then I think you'll have to forward the original one (the one you receive from the Embassy) with a notary's seal on it.

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There might be some documents that you will have to forward though. It was quite some time now when I was processing my last visa, but I know that Japanese Immigration requires documents with a date of issuance not exceeding 3 months. For instance, the birth certificate. You will have to ask your city hall to issue you a new copy of the original. This is what you need to send. I am sure that the company that is processing your visa should tell you precisely what you need.

If I remember correctly , I did not send any original documents but I had my Diploma photocopied and stamped true copy in my university just to make sure, as well as my photocopied transcript of records.

all the rest of my documets were photocopied.

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The immigration is a bit stricter lately but I don't think anything big changed.

Can you not ask your University to have your photocopied documents stamped as true copy ?

As I said in my previous post, I had all my university documents stamped as "true copy" in our secretariat. Meaning that it is certified true copy, same as the original, and the immigration did not question it.

Although, it was a company that applied for me, not a school.