Garuda Indonesia, Merpati Nusantara, Bouraq Indonesia, Sempati Air, and Mandala Airlines operate along a staggering array and number of regular and irregular domestic routes with the main hubs located in Jakarta and Denpasar. Fares are generally so low that air travel becomes a viable option for travel within the country, even for budget travellers. Service is another matter, but with such low fares, most people can't complain. Safety measures are not always a big priority, but this is changing, without a doubt. If you don’t want to arrive at the airport and find yourself bumped from the flight you have to take, we recommend reconfirming all your flight times at least three days in advance.
Only Java and Sumatra, among all of Indonesia's islands, have rail services, and only on Java are they a good alternative to the bus. Rail lines serve all of the major cities on Java, and run the length of the island. Obviously, the faster and more comfortable the train, the more expensive the ticket, but all are generally quite affordable to those on all but the smallest of budgets.
"All aboard.." Crowded Indonesian train
In the more expensive trains, meal cars are available and their offerings fairly inexpensive, whereas on the cheapest trains, hawkers are the best option for meals. Reservations can be difficult to obtain, when the lines serve Java's population of 108 million, and should be made well in advance at any station. For more information, consult a detailed travel guide.
Buses are the dominant form of transportation in Indonesia. They come in various classes starting with economy and heading on up to luxury air-conditioned buses which only tourists can afford. The latter are only present, naturally, in the areas tourists frequent, and on the main highways such as those which link Jakarta to Surabaya and Yogyakarta. These are reserved in advance, through travel agents, and often come with meals and TV.
Economy class buses are very affordable, though the trips can take a long time, as these buses stop at every small cluster of houses along the road. Similarly cheap, but a little faster, are the express buses which make stops only at larger establishments. Seats on these two classes do not need to, and often cannot, be booked. A small matter since they leave stations very frequently.
"Bemos", small trucks much like Thai songthaews, are to be found everywhere and can be hired to take you short or long distances as a comparably priced, and often more fun, alternative to the bus.
Car rental is more or less not an option. Rental agencies are scarce and even if one is found, driving in most parts of Indonesia, especially in the cities, could be the experience which sends one to a mental institution. It is quite feasible to drive yourself in Bali, however. You must have a valid international driver's license and be ready to pay small 'tokens' to police who routinely stop you but, otherwise, it is a good way to traverse the island independently.
Motorcycles are one option for travelling around the cities, although a potentially dangerous one. They can be rented at numerous places, most notably at tourist information centres.
Major routes around the country are serviced by the government owned Pelni line. These routes are only run every two weeks to a month, but are more or less the only option for sea travel to and from the less populated areas of the country. They are, however, quite efficient and comfortable. Five classes are offered, from the ubiquitous "economy" through to first class. The classes are determined mostly by quality of food and number of beds per cabin.
The Pelni Indonesia Site provides information and illustrations on the ships, the fares and the routes.
Regular ferry service, both government and private, runs between all of the islands from Sumatra to the Lesser Sundas and Timor. Outside of this area ferries other than Pelnis are nonexistent.