Effective 01 July 2013, Malaysians holding biometric passport can enter Japan without visa for short term stay up to maximum of 90 days (subject to immigration clearance upon arrival). Non-biometric passport holders must apply for Japan visa as per normal procedures. Biometric passports are indicated with a security chip logo (安全芯片的标志) at the bottom of your passport.
Biometric passports are indicated with the chip logo on the front cover. If your passport front cover does not have this logo, then it is non ICAO compliant. Therefore you will still need to apply for visa.
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