According to the international travel requirements section on the DL website for Malaysian citizens traveling to Japan:
Passport required.
Visa not required for a stay of max. 90 days. However, it is
highly recommended to obtain a visa. Passenger arriving without visa will be subject to thorough interrogation and strict checks by the immigration officers upon arrival and is LIKELY TO BE REFUSED ENTRY.
Visitor must hold:
- return or onward ticket; and
- all documents required for next destination; and
- proof of sufficient funds to cover duration of stay.
If holding an APEC Business Travel Card:
visa not required provided the back of the card states it
is valid for travel to Japan. Upon arrival a visit pass will
be issued.
If you don't have a visa, get one to minimize the hassle. That's a long wait at Narita airport.