Indonesia says asylum seekers were turned back after Australia paid off those who were transporting them.
The boat then broke down and the passengers were rescued by Indonesian authorities.
The Foreign Ministry spokesman said crew members were each given the equivalent of about 3,800 US dollars.
"From the investigation it was revealed that the captain and five of the crew received 5,000 (Australian) dollar each from Australian authorities."
He says if it's true, it would be first time Australia was involved in an incident like this.
Australian Prime Minister Tony Abbott has declined to comment.
The Australian government has promised to stop asylum seekers reaching Australia's shores.
It's turned boats back to Indonesia when it can and sent people to camps in neighbouring countries for long-term detention.