Australia dismisses claims asylum seekers have been mistreated during a boat tow-back operation as video footage surfaced of burnt hands.

Immigration Minister Scott Morrison has warned Australia will not tolerate “sledging” of its navy as Indonesian police investigate claims sailors mistreated asylum seekers during a boat tow-back operation.

Defence chiefs also disputed the claims after the ABC aired footage of asylum seekers receiving medical treatment in Indonesia for burns they allege were inflicted when they were forced to hold onto hot engine pipes during a boat tow-back operation to Rote Island.

Similar footage apparently showing the same group was aired on the Seven Network a fortnight ago.

Immigration Minister Scott Morrison denied the allegations on Wednesday, saying people smugglers had reason to fabricate them to undermine Australia’s border protection policies.

“The Australian government is not going to put up with people sledging the Australian navy with unsubstantiated claims,” Mr Morrison told reporters in Sydney.

“There has been no police investigation in Indonesia. There has been nothing of that sort.

“These are claims that have been made which the Australian government believes … have no foundation,” he said.

However Okto George Riwu, a spokesman for Indonesia’s East Nusa Tenggara provincial police, says officers are looking into the allegations.

“We have no back-up evidence yet that they (the asylum seekers) have been abused,” he told AAP.

Police would begin the probe by searching for the boat crew, who had fled, he said.

“At the moment, we can only do humanitarian help, treating their conditions,” he said.

Navy chief Vice Admiral Ray Griggs took to Twitter to dispute the claims of mistreatment by navy personnel.

“Based on everything I know there is no basis to these allegations – none,” he tweeted.

And acting defence chief Air Marshal Mark Binskin said the safety of life was the paramount consideration during border protection operations at sea.

“I have every confidence in the dedication of our people and their ethical approach to the conduct of operations in difficult and often dangerous conditions,” he said in a statement.

“We are committed to safely executing the lawful direction of government.”

Indonesian MP Tantowi Yahya wants an Australian government investigation and awaits further information.

“But if it is true then the government of Australia has clearly violated human rights of the asylum seekers,” he told the ABC.

Opposition Leader Bill Shorten said the mistreatment reports were concerning but he praised the “extremely tough job” of navy and Customs personnel.

Meanwhile, Customs and Defence have released the terms of reference for an internal review investigating the entry of Australian vessels into Indonesian waters as part of Operation Sovereign Borders.

Mr Yahya refused to accept that the crafts had strayed unintentionally.

“The crew are very trained, plus they are equipped with very sophisticated equipment, so we cannot accept any reasons that they cross other country’s territory unintentionally,” he told the ABC.

He reiterated his views that the coalition’s policy of turning back boats to Indonesia would continue to create tensions between the two countries.