Police in Indonesia have confirmed they are investigating claims asylum seekers suffered burns while under the direction of the Australian Navy.

ABC News has obtained footage of asylum seekers being medically assessed for burns on their hands after they were picked up in Indonesian waters on January 6.

Indonesian police say seven passengers suffered burns during a turn-back operation when Navy personnel forced them to hold onto hot pipes coming out of their boat's engine.

Immigration Minister Scott Morrison said the claims were unsubstantiated, and no investigation has been launched by Indonesian authorities.

But an Indonesian detective this afternoon said police were looking into the asylum seekers' allegations.

Local police from Kupang, where the asylum seekers were taken, say they have statements from the passengers.

Chief Detective Sam Kawengian says the claims warrant investigation and he has invited Australian authorities to travel to Kupang and view the evidence.

He added police have filed preliminary reports about what they have seen and been told by the asylum seekers.

Earlier today Mr Morrison said he would not tolerate people "sledging" Australian Navy personnel, and the claims of abuse were unsubstantiated.

"The Australian Government is not going to put up with people sledging the Australian Navy with unsubstantiated claims when they have high levels of motivation for spinning stories in order to undermine this government's very successful border protection program," he said.

"There has been no police investigation in Indonesia, there has been nothing of that sort."

Speaking to reporters in Sydney, Mr Morrison also attacked the ABC for broadcasting the claims.

"I think the mere publication of things that are clearly so unsubstantiated I think is very unfortunate," he said.

In an interview with Fairfax Radio, the minister repeated his concerns about the report.

"I want to address something pretty appalling that was being reported by the ABC this morning - airing unfounded, unsubstantiated, outrageous allegations against our Navy and our Customs and our border protection service," he said.

"I mean there [has] been no police investigation in Indonesia."

MP says Australia should guarantee safety

One Indonesian MP has told the ABC that Australia should guarantee the safety of all asylum seekers.

"The country of destination should protect them," MP and foreign affairs commission member Tantowi Yahya told 7.30.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 8 minutes 10 seconds 8 m Watch Tantowi Yahya's interview on 7.30

"There should be a guarantee that they will not experience any physical abuse or torture or something like that.

"Whoever comes to our country, regardless of their intention, they still need to be protected."

He said the burning allegations had not been "clarified" but said that "if it is true" then "the Government of Australia has clearly violated the human rights of the asylum seekers.

"Your government still has to clarify whether this is true or not," he added.

Truss confident military acted 'appropriately'

Acting Prime Minister Warren Truss also says he is confident Defence Force personnel acted responsibly.

"I regret the fact that some asylum seekers seem to have been injured, but who knows under what circumstances that injury happened," he said.

Sorry, this video has expired Asylum seekers allege physical abuse by Navy

"The Defence Force, as a routine, looks at its operations from day to day. I am confident that they have behaved responsibly and appropriately."

But Opposition Leader Bill Shorten says the Government is putting Australia's Defence personnel in a difficult position.

"Whilst the reports are concerning, and they are very concerning, we also stand up and recognise that our military personnel have an extremely tough job," he said.

"But their tough job is made even harder by the Abbott Government's policies."

Boat passenger Merke Abdullah Ahmed, from Somalia, claims Australian Navy personnel punched some passengers and others were forced to hold onto the hot metal.

"They physically harmed us. Some of the passengers onboard, they tried to complain and speak about just their problems. They just punched [them] ... and, you know, fall down on the ground," he said.

EDITOR'S NOTE: ABC News has issued a note about aspects of this coverage: http://about.abc.net.au/press-releases/abc-statement/