Australian women, children and elderly Australians have been stranded at the southern end of the Bali Archipelago for days on end.
The rescue effort has now reached a saturation point.
The island of Bali is one of the world’s most popular holiday destinations.
More than 4,000 people are living in the islands temporary shelters.
The Government of Balingas rescue mission is now the largest in the world.
Key points: The International Organisation for Migration (IOM) says around 3,500 people have been rescued and more than 800 people have died on the island since the start of the crisis.
The first batch of arrivals have been flown to the capital Bali, where they will be sent to centres in Papua New Guinea and Nauru.
IOM says it is expected the number of arrivals to continue to rise as rescue operations intensify.
Authorities have warned of a “tremendous risk of further deterioration” to the island as the rescue effort continues.
A senior police officer said on Friday that the death toll had risen to at least 577.
More than 80,000 asylum seekers have arrived on the Indonesian island since Christmas, most of them from Myanmar.
Last week, Indonesia imposed a nationwide state of emergency, requiring local authorities to establish safe zones.