The Indonesian navy has reportedly turned away a boat filled with hundreds of the migrants, claiming that its passengers wanted to reach Malaysia instead.
Indonesian navy spokesman Manahan Simorangkir said that the vessel had been provided with food, water and medical supplies before being sent back to sea.
However, the International Organization for Migration said that the decision was “shocking” and that “these people need to land”.
Joe Lowry, an IOM spokesman, told the BBC that people on the ships were likely to be suffering from serious illnesses and required “immediate humanitarian assistance”.
The current crisis has been precipitated by recent regional crackdowns on people smuggling activities in the region. Profiteers promising safe crossing to desperate passengers hoping to reach Indonesia, Thailand or Malaysia have abandoned many boatloads at sea.
Fearing the intervention of authorities, brokers and agents have been going into hiding, meaning that refugees cannot disembark, even when they have made substantial payments to smuggling networks.
Many of the passengers of the boats – often rickety wooden vessels – are of the Rohingya ethnicity. Rohingyas are a Muslim group mainly living in Myanmar, suffering persecution and minimal human rights protections.
Attacks on the Rohingya people have intensified over the past three years, according to the Huffington Post. More than 140,000 of the 1.3 million Rohingya population have been forced from their homes, with many now living in refugee camps.