The major ports of entry are mainly cities of Jakarta, Surabaya, Medan and Denpasar. Visitors can choose the ports of entry or landing according to their destinations.
Entering and Leaving Malaysia: There are many ferries shuttling between Malaysia and Sumatra. There are comfortable speedboats between Penang of Malaysia and Belawan near Medan of Sumatra. Most passengers take this route (RM90) to enter Indonesia. There are also passenger ferries between Dumai of Sumatra and Malacca of Malaysia with the price of 140,000RP. Passenger ferries between Pulau Batam of Sumatra and Kuala Tungkal of Malaysia charge 80,000RP. On the east coast of Kalimantan, there are many speedboats from Tarakan to Nunukan (82,000Rp), and from Nunukan to Tawau (110,000Rp) every morning.
Entering and Leaving Papua New Guinea: You can rent a boat to go from Djajapura of Indonesia to Vanimo of Papua New Guinea. Check if you need a visa for entering Indonesia.
There are scheduled ferries sailing between Sumatra Island, Java Island, Bali Island and Nusa Tenggara. Pelni, a passenger ferry company has sailing routes that cover everywhere within the country.
Pelni is the national shipping company of Indonesia. It has modern passenger fleets, and the routes cover major ports of Indonesia and most of the remote areas of the islands. The routes and schedules change frequently, but they are all available for checking on their website. There are four classes of passenger cabins, including economic cabins as well, originating from the old-style deck cabin. The first class (Class I) is the superior cabin with only two beds in each cabin with the relatively higher price. Class IV cabin has 8 beds in each cabin. The economic cabin is suitable for short-distance journeys. You can book tickets two weeks ahead at the most, and usually you should book the tickets several days in advance.
On other remote outlying islands, you need to relax and be patient to wait for ferries which happen to pass by. You can also contact the local port office and shipping company. Of course, you can also arrange some unusual sea voyages. On the sea area of Indonesia, you can still see those old-style Makassar sailing boats. You can take this kind of boat from Sulawesi to some other islands, especially Java Island.