Asylum seekers have accused the Australian Navy of beating them and inflicting burns by ordering passengers onboard a boat being towed back to Indonesia to hold on to parts of the engine.

The claims of physical abuse come as Canberra is warned that it risks clashes with Indonesia at sea over the Australian Government’s asylum seeker policies and the admission that Australian ships have entered Indonesian waters without permission.

ABC News has obtained video footage of asylum seekers receiving medical assessments of burns that Indonesian police say were inflicted by the Australian Navy.

The Federal Government denies the claims, but Indonesian police say they had to get treatment for 10 asylum seekers, seven of whom had severe burns on their hands after they were picked up in Indonesian waters on January 6.

Indonesian police say the burns were from being forced by Navy personnel to hold onto hot pipes coming out of the boat’s engine.

The video and the version of events given by the police seems to back up the claims of mistreatment made by the asylum seekers when they first spoke to the ABC a fortnight ago.

Immigration Minister Scott Morrison has released a statement, saying he would not comment on confirming specific operations but, “the Government rejects any allegation of inappropriate behaviour by our navy or Customs and border protection personnel in the conduct of their duties”.

“Smugglers and their clients have strong motivations for seeking to discredit the activities of Australia’s border protection operations in an attempt to undermine public support for the Government’s strong border policies.”

Territorial breaches ‘unlikely unintentional’

Meanwhile, a former Indonesian general and current member of Indonesia’s foreign affairs commission says it is impossible that Australian Navy ships ended up in Indonesian waters without intending to, as Immigration Minister Scott Morrison and his border protection chief have claimed.

Mr Morrison said in a briefing last Friday that the Australian Government had apologised to Indonesia after admitting vessels operating under its border protection policy had “inadvertently” breached Indonesian territorial sovereignty “on several occasions”.

He said he was told last Wednesday that “border protection command assets had in the conduct of maritime operations associated with Operation Sovereign Borders inadvertently entered Indonesian territorial waters on several occasions” and blamed the incursions on “positional errors”.

Lieutenant General Angus Campbell, the commander of Operation Sovereign Borders, said that although an investigation had been launched into the breaches, he was confident they were unintentional.

“I believe our people were acting in good faith at all times,” he said of the incursions, adding that the agencies involved in Operation Sovereign Borders regretted “any affront to Indonesia these events may have caused”.

However, Tubagus Hasanuddin said experience and training told him that the incursions were unlikely to have been unintentional, as Australia claimed.

“I studied in Australia – in the military academy. The Australian Navy doesn’t have wooden boats, they have warships equipped with modern technology,” he said.

“They should have known which part of the water is Indonesia and which is not.”

The Indonesian government is yet to say if it has accepted Australia’s apology for the incursions, but it has sent four navy ships to patrol its maritime borders to the south.

The retired general says if Australia keeps forcing asylum seeker boats into Indonesian waters, it risks meeting the Indonesian navy head to head on the high seas.

“In my opinion, this will result in tension between nations,” he said.

“And it’s not impossible a clash between Indonesia and Australia national forces, and I believe that this needs to be avoided. It can’t happen.

“So it’s better that Abbott meets again with president (Yudhoyono) and sit together to find the best solution.”