Raja Ampat is accessed via Sorong, a city situated on the far western tip of Indonesian West Papua. Sorong is a quite peaceful city although it's growing quite fast. The airport is quite small but on arrival we always make sure you're greeted by someone. Getting to Sorong is surprisingly straight forward.
We currently have two preferred options.
A morning flight from Australia will arrive in Jakarta sometimes in the middle of the day. Flights to Sorong are then either direct or via Makassar and depart late evening and travel overnight, arriving about 7AM. So we usually organise a day-room in a nearby airport hotel with check out at 6pm, then after dinner, proceed back to the domestic airport. Return flights again, are via Jakarta and usually connect on the same day (again with a stop over where a day room can be arranged nearby) and overnight back into Australia.
Another pleasant way to travel we find, is to arrive in Bali and then catch an afternoon connecting flight to Makassar. Makassar is a main destination hub and the airport is well serviced. A one-day stop-over there is sufficient time to visit Rammeng Rammeng, about an hour from the airport, which is beautiful limestone karst scenery. It breaks the journey up quite pleasantly as the flight to Sorong departs at about 3:30AM. There is a very basic Ibis airport hotel about a minute walk from the domestic airport terminal which, although a little noisy, can be convenient. We would usually take the flight back via Jakarta to Australia.
Airports in Indonesia