There is currently no passenger sea travel between the Philippines, Papua New Guinea and Indonesia.
Major cruise lines often run cruise ships between Bali and Australia.
There are regular ferry services between Dili in Timor-Leste and Oecussi, which borders West Timor. If crossing into Indonesia from Oecussi, you will need to have organised your visa already in Dili.
Regular and comfortable high-speed ferries run the two-hour journey between Melaka (Malaysia) and Dumai (Sumatra). From Johor Bahru in southern Malaysia, daily ferries run to Pulau Bintan in Sumatra's Riau Islands.
Ferries and speedboats connect Tarakan and Nunukan in East Kalimantan with Tawau in Sabah. For these routes you'll need a visa in advance.
From Batam, speedboats travel to Tanjung Buton with minibus connections to Pekanbaru on the Sumatran mainland. Otherwise, Pelni ships pass through Batam to and from Belawan (the port for Medan) and Jakarta.
Boats also travel between Pulau Bintan and Singapore. Service includes Bintan Resort Ferries (www.brf.com.sg).