Yes, Imperial Japan did invade Malaysia and Singapore from the sea. How else Borneo was taken by Imperial Japan in 1941-1942?Japan did not invade Malaysia and Singapore via amphibious assault. They did a blitzkrieg style attack coming down from Thailand.
Philippines was a cakewalk because it happened right after Pearl Harbor and the imperial Japanese air force had quickly achieved air superiority with the destruction of Clark airbase.
Speaking of Peninsular Malaysia - Other than coming down from the north through Thailand, the IJA and IJN troops also conducted amphibious assaults on Pattani, Songkhla (both in southern Thailand) and Kota Bahru (in northern Peninsular Malaysia) just in case Thailand didn't lay down their arms and fight against IJA troops that were invading them through Indochina.
Speaking of Singapore - The British troops blew up the only land crossing between Malaysia and Singapore, i.e. the Causeway after completing their retreat from Johor Bahru into Singapore. The IJA troops had to conduct two simultaneous amphibious assaults across the Johore Strait to invade Singapore from the west and north of the island.
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