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The embassy of Japan in Malaysia states :
Criteria to apply visa in Malaysia
Foreigners (non-Malaysian nationals) who wish to apply for Japan visa at the Embassy of Japan in Malaysia must meet the criteria below:
You are a permanent resident in Malaysia with My PR card or
You have a valid Malaysia long term visa (one year visa and above) in the passport, e.g. employment/ student/ dependent/ MM2H visa/ Residence pass.
Please take note that Embassy of Japan in Malaysia do not accept visa applications from those who are under short social visit pass such as tourists, short-term business travelers and foreigners transiting in Malaysia.
You need to go back to India to apply for your visa