This continued well into the 20th century, until relations reached an abrupt nadir with the rise of the Empire of Japan and its subsequent invasion and occupation of British Malaya and Borneo during World War II, during which the local populace endured often brutal Japanese military rule.

According to a 2013 Pew Research Center survey, 80% of Malaysians hold a positive view of Japan and its influence, ranking Malaysia as one of the most pro-Japanese countries in the world.

Its maritime trade with kingdoms in Southeast Asia included Japanese products—silver, swords, fans, lacquerware, folding screens—and Chinese products—medicinal herbs, minted coins, glazed ceramics, brocades, textiles—were traded for Southeast Asian sappanwood, rhino horn, tin, sugar, iron, ambergris, Indian ivory and Arabian frankincense.

[4] In the 20th century, Japan established itself as an imperial superpower and launched offensives throughout Southeast Asia, including Malaya, a British colony at the time.

The local population found inspiration for independence from witnessing the ability of Imperial Japan to expel the Europeans from Southeast Asia.

Significant support for the Japanese deteriorated and the British were able to regain Malaya, Singapore as well as North Borneo at the end of World War II.

With its defeat and subsequent occupation at the hands of the United States, Japan sought to re-establish diplomatic relations with its neighbouring countries.

[15] Both Japan and Malaysia are members of East Asia Summit, Asia-Pacific Economic Cooperation,[16] ASEAN+3 and World Trade Organization.

In September 2016, the Japanese government, through Prime Minister Shinzō Abe, provided Malaysia free patrol boats following similar agreements with the Philippines and Vietnam.