With the purchase of new passenger transport vessels, PELNI, the state-owned shipping company, now has six modern ships serving all main ports from Banda Aceh in the westernmost tip of the country to Sorong in Irian Jaya in the East. Built to accommodate 1000 to 1500 passengers in four classes, the ships are air-conditioned, whereas first class cabins have attached bathrooms and TV sets. Not luxurious but comfortable, the ships offer an alternative to flying and is a more leisurely form of travel. There are regular schedules and routes, all touching in at Jakarta their main base.

Foreign cruise lines operate in Indonesian waters, though not regularly. A 40-passenger luxury cruise ship, the MV Island Explorer, offers trips to the eastern Indonesian islands from Bali part of the year, and from Jakarta to Sumatera the rest of the year. There are also ferries between islands, though comfort may not be as desired. For adventure travellers, a ride on a Pinisi Bugis schooner could be exciting if advance arrangements are made. One of the last sailing fleets in the world, about 3,000 of these schooners still ply between islands, trade goods as they have been for centuries.