The gateway to Raja Ampat is Sorong, in West Papua, reached by direct flights from several Indonesian cities including Jakarta, Makassar, and Manado. From Sorong, a fast ferry runs to Waisai, the administrative capital of Raja Ampat, taking about three hours and departing daily. Waisai itself is small and mainly exists as a ferry terminal and permit office — most travellers head straight for the dive resorts or their liveaboard.
Getting to Sorong from Europe involves at least two connections and typically 24–30 hours of travel. From Australia it is easier: flights from Darwin or Cairns to Denpasar or Makassar connect to Sorong. The total journey is demanding, which is part of why Raja Ampat remains comparatively uncrowded.
A conservation permit is required on arrival at Waisai, paid in cash. This fee goes directly to local reef conservation efforts and is not optional. Check the current amount before you go as it changes periodically.