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Marty Natalegawa. Picture: Reuters

Indonesian leaders have played down claims the country could become embroiled in a military stand-off with Australia, but again underlined their anger over Prime Minister Tony Abbott's border security regime.

The shift came amid suggestions the Australian military provided medical treatment to an asylum seeker who received burns to his hands during a turn-back operation.

Australian officers also performed a "quick assessment" of the asylum seeker's claims of abuse and determined there was no substance to them.

Speaking at the World Economic Forum in Switzerland, Indonesian Foreign Affairs Minister Marty Natalegawa said Australian and Indonesian relations were going though a "difficult patch".

Dr Natalegawa appeared to confirm reports a number of Indonesian navy warships have been deployed and air force radars were being readied to monitor waters between Indonesia and Australia.

But he insisted relations were in a "good state".

"It's just a country that is keen to ensure our sovereign border is properly protected," he said. "It's not meant to be an unfriendly act to anyone."

It is understood the Indonesian military is in the grip of a fuel crisis and is unable to provide enough fuel for basic air force and naval operations.

Indonesian leaders have made clear their anger over admissions Australian warships accidentally sailed into Indonesian waters - most likely during a turn-back operation.

Mr Abbott has rejected claims Australian navy personnel abused asylum seekers by forcing them to keep their hands on a hot boat engine as their boat was towed back.

But Mr Abbott has refused to detail how he can be sure no abuse occurred.

The Weekend West understands officers at Border Protection Command carried out a basic assessment when the allegations were aired and found they did not stand up.

The West has also been told navy personnel applied basic first aid to the burns.

News Limited reported the asylum seekers might have injured themselves trying to sabotage their own engine.

Immigration Minister Scott Morrison said yesterday it had been 36 days since an asylum boat arrived in Australia - the longest period of no boat arrivals since March 2009.