To get to Raja Ampat you should first take a flight from Jakarta or Makassar to Sorong. There are small aircrafts to take you to Waisai, capital of the district of Raja Ampat, or alternatively you can take a ferry from the port of Sorong to the islands.
Established in 2012, the Marinda Airport in Waisai, the capital town of Raja Ampat Regency served flights to and from the city of Sorong. Wings Air served daily flight between Sorong and Raja Ampat, while Susi Air flight twice a week on Monday and Saturday. Please be advised that the Marinda Airport is still under development and expansion and located relatively far from any facilities. So be sure to pack some snacks and drinks as you await your return flights to Sorong.
Alternatively, there are ferries available to get you from Sorong and Waisai and vice versa. The ferry trip will take about 2 to three hours.
As the main hub to Raja Ampat, the Domine Eduard Osok Airport in Sorong serves flights to a number of major cities in Papua and Indonesia including Manokwari, Jayapura, Ambon, Makassar, Manado, and Jakarta.
Garuda Indonesia operates daily flights between Jakarta-Sorong. As do Sriwijaya Air and Nam Air, Where as Batik Air flies twice daily between Jakarta and Sorong.