The revelation comes as real Rohingya refugees took to the water to escape persecution in Myanmar and crowded camps over the border in Bangladesh, the ABC News reported.
Brigadier General Herry Rudolf Nahak said the men were, in fact, Bangladeshis working in Malaysia who were convinced by the people smugglers that they would earn more money in Australia.
Indonesian police said one of the three alleged people smugglers was a Rohingya man. The other two were Bangladeshi and Indonesian.
The Indonesian police have named three suspects, including a Rohingya man, as the organisers of a 'complex scheme' to bring people to Australia illegally. Police managed to unearth the ring with the help of Australian Federal Police.
The report said quoting the director of general crime with Indonesia's national police that "people smugglers organised fake papers for six Bangladeshi men who were initially brought by speedboat from Malaysia."
"After a long journey through Kalimantan and Java, they were eventually smuggled to the Papuan port of Merauke because it was closest to Australia," the ABC
"The organisers then planned to hire a local fishing boat to bring the men to the Australian mainland," ABC News said.
Communities in Indonesia helped the men in their journey because they claimed to be fellow Muslim Rohingya fleeing persecution in Myanmar.
Police said, "Sympathetic members of one Indonesian community even raised money to buy plane tickets for the men to fly to Merauke."
The report added that 'the scheme came undone' when Papuans in Merauke became suspicious and reported the strangers to local police.
The Bangladeshi men were picked up late last year and detailed the scheme to authorities.
They are now living in witness protection in Indonesia ahead of a trial of the alleged people smugglers. This is the first time details of the police operation have been released.
Brigadier General Nahak said this was an international operation.
"Indonesian Police are working together with the AFP and NZ police, as [this matter is also in their] interest because they're the destination countries (of the people smuggler) and Indonesia was a transit country for the people-smuggling operations," he said.
Indonesian police said they seized ATM cards, airline tickets and cash equivalent to $A16,000 or over Tk 1 million from the men.
News of the scam comes as legitimate Rohingya refugees fleeing Myanmar take advantage of calmer seas to attempt to enter Malaysia and Indonesia by boat. Late last week, 76 refugees were rescued on a boat off Indonesia, which had been adrift for nine days.