The Abbott government faces the tough task of rebuilding Australia's relationship with Indonesia following the executions of Bali Nine pair Andrew Chan and Myuran Sukumaran.

All sides of Australia's politics have united to condemn Indonesia's decision to carry out the shootings, with Labor urging a stronger response from Canberra.

Chan and Sukumaran were executed by firing squad alongside six other prisoners after midnight (3am AEST) in a field on Nusa Kambangan.

The government's reaction was swift, with Indonesia ambassador Paul Grigson recalled from Jakarta.

The bodies of the executed inmates arrive in Cilacap, en route to Jakarta. (9NEWS)

Indonesia has brushed off the move, with Attorney-General HM Prasetyo labelling it a normal diplomatic response.

Prime Minister Tony Abbott, who has strongly condemned the executions, wants his foreign policy more strongly focused on Jakarta, but the relationship has been damaged in recent months by the Bali Nine executions and earlier revelations Australia had been spying on Indonesia's leaders.

To that end, Mr Abbott has asked Australians not to make their condemnation of the executions "personal".

"I regard myself as a friend of Indonesia and my hope is that this presidency is a successful one," he said.

"While this is a dark moment in the relationship, I do hope it (the relationship) will be restored."

However, Labor has called for stronger reaction from the government.

Bill Shorten said the executions were not "justice", while deputy Tanya Plibersek said "we have been ignored".

Greens leader Christine Milne has also condemned Indonesia's actions.

Indonesia's attorney general Muhammad Prasetyo. (Supplied)

Bill Shorten has urged the government to a stronger response on the Bali Nine. (9NEWS)

Labor deputy leader Tanya Plibersek joined the condemnation. (9NEWS)

Mr Prasetyo earlier defended the executions, saying it was necessary "to save the nation from the danger of drugs".

"We are fighting a war against horrible drug crimes that threaten our nation's survival," Muhammad Prasetyo said.

"I would like to say that an execution is not a pleasant thing. It is not a fun job.

"But we must do it in order to save the nation from the danger of drugs. We are not making enemies of counties from where those executed came. What we are fighting against is drug-related crimes."

Mr Prasetyo made the comments at the port of Cilacap, where boats leave for the high-security prison island of Nusa Kambangan, where Bali Nine ringleaders Myuran Sukumaran and Andrew Chan were executed hours earlier.

Former Foreign Minister Bob Carr criticised the Abbott government's decision on Sky News Australia's PM Agenda program, telling host David Speers it put "Australian lives at risk".

IN PICTURES: Sukumaran and Chan's final journey View Gallery

"I don't think withdrawing the ambassador is in Australia's interests," Mr Carr said.

Mr Carr said the Australian government is now stuck with the question of when to reinstate the ambassador.

"Cooperation with Indonesia is hugely in Australia's interest," he said.

Mr Carr said Australia had an ongoing relationship with Indonesia working on immigration, counter-terrorism and human rights.

From suburban Sydney to death row: The tragic journey of Myuran Sukumaran and Andrew Chan View Gallery

"We've got more diplomats (in Indonesia) than we do in Washington (DC), that indicates the workload," Mr Carr said.

Mr Grigson has only been in the position since January, and was considered a senior appointment at a tumultuous time in the diplomatic relationship.

He is expected to return to Australia at the end of the week.

The bodies of Chan and Sukumaran are now en route to Jakarta, where repatriation arrangements will be made.

IN PICTURES: How newspapers around Australia reported on the Bali Nine executions View Gallery

The deaths have been marked by international condemnation of the death penalty and of Indonesia's actions.

Bali Nine smuggler Myuran Sukumaran's art from death row View Gallery