Passengers who were turned back from Australia's north on New Year's Day say the Navy fixed their boat's engine and forced them back to Indonesia
In the process, they say some people were punched, beaten and burnt.
Australia has denied any inappropriate behaviour by its sailors.
Correspondent: George Roberts, Indonesia Correspondent
Speaker: Merke Abdullah Ahmed, asylum seeker; Tubagus Hasanuddin, former general and current member of Indonesia's Foreign Affairs Commission
GEORGE ROBERTS: Just before Christmas and again early this year, asylum seeker boats turned up on Indonesia's Rote Island. Both groups said they were forced back by the Australian Navy.
Passengers like Somali man Merke Abdullah Ahmed gave similar stories.
MERKE ABDULLAH AHMED (translated): Yeah, they physically harmed us. Some of the, you know, passengers on board, they tried to complain and speak about just their problems. They just punched on, you know, and punched physically and, you know, fall down on the ground.
GEORGE ROBERTS: He said some passengers were forced by the Navy to hold onto hot metal.
The claims were hard to verify. Now footage taken that week and obtained by ABC News shows medics inspecting what appears to be severe burns and blisters on the palms of several asylum seekers' hands.
Police from Rote Island have confirmed they took 10 asylum seekers for medical treatment; seven had similar harsh burns. In the video, the Indonesian medics ask what caused it.
INDONESIAN MEDIC (excerpt from footage): Okay, which part of the engine?
GEORGE ROBERTS: The local police chief backs the asylum seekers' story that the Australian Navy made them hold on to a hot engine pipe.
Earlier this month the Australian Immigration Minister Scott Morrison confirmed that Australian sailors are no longer personally liable for what's done under Operation Sovereign Borders.
Merke Abdullah Ahmed again.
MERKE ABDULLAH AHMED (translated): Well every question we asked of them they said: we don't know, it's the instructions of the government, those who decide, the big decisions.
GEORGE ROBERTS: A spokesman for Scott Morrison has provided a statement in response to the mistreatment claims, saying Australian sailors have acted appropriately.
STATEMENT FROM SCOTT MORRISON (voice-over): While not commenting or confirming any specific operations, the Government rejects any allegation of inappropriate behaviour by our Navy or Customs and Border Protection personnel in the conduct of their duties as part of Operation Sovereign Borders.
Smugglers and their clients have strong motivations for seeking to discredit the activities of Australia's border protection operations in an attempt to seek to undermine public support for the Government's strong border policies.
GEORGE ROBERTS: Now there are two navies patrolling that piece of ocean. After Australia's admission that it inadvertently breached Indonesia's territorial waters while trying to stop asylum seeker boats, the country has sent four navy ships to the area.
A former Indonesian General and current member of the country's Foreign Affairs Commission, Tubagus Hasanuddin, says it's impossible for Australian ships to accidentally stumble into Indonesian waters.
TUBAGUS HASANUDDIN (translated): I studied in Australia, in the military academy. The Australian Navy doesn't have wooden boats; they have warships equipped with modern technology. They should have known which part of the water is Indonesia and which is not. There should not be any more breaches from their Navy and excuses like the radar isn't working or something - that's bullshit.
GEORGE ROBERTS: Tubagus Hasanuddin was military advisor to three Indonesian presidents. He says if Australia keeps pushing boats back to Indonesia, it risks a mid ocean disaster.
TUBAGUS HASANUDDIN (translated): Firstly, if they push back these people and kill them in the sea in doing so, it's fully their responsibility under the international law.
Secondly, in Indonesia officials have started to get angry. They refuse to talk about Australia. It's possible that if it happened again, our Navy will face them head to head. We're not talking about who will win or lose, but every country has the right to protect their territory.
GEORGE ROBERTS: Indonesia won't yet say if it's willing to accept Australia's apology for violating its territory.