Police said the crew discovered 64 live parrots and 10 dead birds after hearing noises coming from inside a large box.
Indonesia is home to the highest number of threatened bird species in Asia and a rampant illegal trade in birds.
Birds are sold domestically in giant avian markets or smuggled abroad.
The destination of the parrots found on Thursday morning in the port town of Fakfak was unclear, local police spokesman Dodik Junaidi told AFP news agency.
