Star striker Faizal Saari scored two goals to lead the Malaysian charge, while five others made an entry in the scoresheet.
Japan denied the dominant Malaysian strikers a goal until the 23rd minute when Niman Nik Rosemi opened the account with a field goal.
Rashid Baharom, Nabil Noor, Firhan Ashari and Fitri Saari were the other scorers for Malaysia, who had defeated defending champions Pakistan 4-2 and China 5-1 in earlier matches.
In the round-robin league standings, Malaysia is followed by India on seven points from three matches. Pakistan and China are on three points from three outings.