Yes. You must pay customs duty when importing goods into Japan if your goods exceed JPY 10,000 (approximately 310 myr)
Following the de minimus rule of Japan, imports exceeding this JPY 10,000 are subject to customs duty, whereas those below it are duty-exempted.
Malaysia and Japan have an economic partnership agreement which allows both countries to enjoy certain benefits by eliminating tariffs on specific agricultural, industrial, forestry and fishery products.