From 1 July 2013, Malaysian DOES NOT NEED a Visa to visit Japan provided that they hold ordinary biometric passports with embedded microchip that is compliant with ICAO standards. All Malaysian passport issued from February 2010 are compliant with ICAO standards.
Malaysian can enjoy visa free entry to Japan up to 90 days.
However, for Malaysian who plan to work in Japan or stay more than 90 days, you are still required to apply for a visa to enter Japan.
Airasia now operate flight to Tokyo (Haneda Airport), Osaka (Kansai Airport) and Nogaya (Chubu Airport). Now everyone can go Japan!
Malaysia Airlines on the other hand fly to Tokyo from Kuala Lumpur and Kota Kinabalu. With Visa free entry and low exchange rates for Japanese Yen, extra direct flights to Japan from Kuala Lumpur and Kota Kinabalu in Malaysia now is the best time for Malaysian to visit Japan. Just make sure you have a Malaysian passport with microchip as shown in the picture above. Then you can visit Japan without first applying for a visa.