TIMATIC (
http://www.delta.com/travel/trav_ser...atic/index.jsp) shows for Malay citizens visiting Japan:
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.
As A U.S. Citizen, I have had layovers in Japan of 3 or 4 hours that I used to at least get to the rest of the airport
(there's very little to do in the International Terminal). Once, I actually put on the landing card "Purpose of Visit: Lunch"
The immigrations officer thought it was funny.
Sounds like it is the best plan to get a visa, although shore passes are available if you don't have time to get the visa and want to risk it. Of course, the worst that can happen is you'll be denied entry and stuck in the airport which would be the case anyway!