Indonesia has good ferry connections with Malaysia and Singapore, and there are frequent cargo boats from the Philippines

From Malaysia and Singapore
A variety of ferries and speedboats depart from Penang , on the west coast of Peninsular Malaysia, to Medan and from Melaka , south of Medan, in southern Malaysia, to Dumai . You can also take ferries from...
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From the Philippines
Every week or so a cargo boat leaves General Santos in the Philippines for Bitung in Northern Sulawesi . It's a rough ride shorn of any sort of comfort, but at around US$30 one-way, it's a lot cheaper than flying .
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