You can visit notary public office in Japan
Assumed that you are Indian living in Japan. Then, you hope to convert private document (ex. diploma issued by University in Japan) into Official document, you can take these process.
1 You can visit notary public office in Japan with diploma, ID.
2 Notary public will notarize the documents.
You can make statutory declaration paper at Notary public office
If notary public tries to notarize diploma certificate itself, you need to receive additional document from president of university and it should be difficult.
So, alternatively, you can make declaration at notary public office.
You do not need to visit embassy in Japan
Assumed that you submit the diploma to India.
India is participating in Hague convention.
So, you do not need to visit embassy of India in Japan.
Document issued by notary public in Japan is available in India.