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Bali Nine: Australia makes official complaint to Indonesia over photos of police chief with Andrew Chan and Myuran Sukumaran

Australia has lodged an official complaint to the Indonesian government over photos of the Denpasar police chief posing with condemned drug smugglers Andrew Chan and Myuran Sukumaran.

The photos have been published in local and international media of Commissioner Djoko Hari Utomo on the flight with the pair from Kerobokan prison in Bali to Central Java.

The Commissioner has told Fairfax Media that he was trying to raise the spirits of the Australians and had no idea the photos were being taken.

The ABC understands the Indonesian ambassador is in Perth and will be phoned by the Department of Foreign Affairs and Trade.

The secretary of the department, Peter Varghese, lodged an official complaint over the photos and the disproportionate use of force in the transfer of the two prisoners.

The complaint was also lodged in Indonesia by the Australian ambassador.

Liberal MP Philip Ruddock expressed his disappointment in the photos.

"Obviously each of them were, in their own ways, very concerned and to have a smiling police officer photographed, either with a hand on the shoulder or endeavouring to engage them in conversation, I think is unfortunate," he said.

Foreign Minister Julie Bishop earlier described her shock at the force used during the transfer from Kerobokan prison to Nusakambangan island.

"I just cannot comprehend it. They are two men who are described by their own prison governors as model citizens, two gentlemen who pose no risk to anyone," she told the ABC's AM program.

"I cannot comprehend the manner or the method of their transfer to the so-called execution island."

It earlier emerged Ms Bishop made an eleventh hour bid to save Chan and Sukumaran by proposing to repatriate three convicted Indonesian drug criminals in return for the lives of the two men.

It is understood Indonesia did not accept the offer during a tense phone call on Tuesday between Ms Bishop and her Indonesian counterpart.

Indonesian president Joko Widodo has confirmed the prisoner swap will not be considered, telling local media Indonesia wants to be friends with any country but sovereignty still applies.

His comments came after Indonesian foreign ministry spokesman Armanatha Nasir said there was no legal basis for Indonesia to act on the proposal.

"Basically because Indonesia does not have any legislation or law or any other legal instruments that would enable the issue of prisoner exchange," he said.

"So there's no legal framework for Indonesia to be able to take a legal prisoner exchange.

"This idea was put forward to our minister two days ago and we told them [Australia] then."

Relatives of Chan and Sukumaran have arrived in Central Java to arrange prison visits with the men ahead of their executions.

Members of the Chan and Sukumaran families flew into Yogyakarta airport before driving to Cilacap and were being supported by consular officials from the Foreign Affairs department.

The relatives will make arrangements to go from Cilacap to Nusakambangan, where the two Australians are awaiting announcements by the Indonesian government on when the executions will be carried out.

Abbott urges Indonesia to 'pull back from the brink'

Indonesia's president Joko Widodo has indicated that will not be this week, but said he had a constitutional responsibility to follow through with the executions.

Prime Minister Tony Abbott questioned how it could be in Indonesia's interest to kill the men.

"As a government, as a parliament that wants nothing but good for Indonesia, we are speaking as one united voice publicly and privately in every way we can — pull back from this brink," he told Parliament.

"Pull back from this brink. Don't just realise what is in your own best interests, but realise what is in your own best values."

Opposition Leader Bill Shorten echoed those sentiments.

"Some people have said to me, 'But it's drugs, people know the law of the land they travel into and really that's all that you can expect in this matter'," he told Parliament.

"What I would say is that — and this Parliament I genuinely believe supports — the death penalty will solve nothing.

"The execution of these two young men will solve nothing."