The food manufacturing industry in Malaysia plays a significant role in the economy. Since the industry is dominated by small and medium-sized enterprises, the local food manufacturing sector is not able to satisfy increasing demand. Malaysia has experienced a persistent food trade imbalance as the demand for food items has risen faster than their supply. In helping Malaysia become more self-sufficient in its food requirements, improvements in the supply chain are important. Given that Japan is a supply chain superpower and for years has been an important trading partner for Malaysia and contributes capital, technology and management expertise to it, its supply chain management practices need to be closely studied. Supply chain management was studied using a qualitative survey involving several Japanese food companies operating in Malaysia. The main aim of this paper is to explore the underlying problems concerning supply chain management that Japanese food companies in Malaysia experience. The approaches with which Japanese food companies overcome these problems are examined.