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Australia today took the unprecedented step of recalling its ambassador to Indonesia after two of its citizens, Myuran Sukumaran and Andrew Chan, were executed for drugs offences.

Prime Minister Tony Abbott said the relationship with Jakarta "has suffered as a result of what’s been done over the last few hours".

"We respect Indonesia’s sovereignty but we do deplore what’s been done and this cannot be simply business as usual," he told reporters.

"For that reason, once all the courtesies have been extended to the Chan and Sukumaran families our ambassador will be withdrawn for consultations."

Sukumaran and Chan, the ringleaders of the "Bali Nine" heroin trafficking gang, were executed by a firing squad on the high-security prison island of Nusakambangan in the early hours today, Foreign Minister Julie Bishop confirmed. They were sentenced in 2006. Five other foreign drug convicts and one Indonesian suffered the same fate.

Australia has never recalled an ambassador over a drug execution before, even during the high-profile case of 25-year-old Nguyen Tuong Van, who was put to death by Singapore in December 2005.

However, the executions were "both cruel and unnecessary", Abbott said, necessitating the "unprecedented" move to bring back Ambassador Paul Grigson. Ties were only just recovering after sinking to their lowest point in years in late 2013 after reports that Australian spies tried to tap the phones of then president Susilo Bambang Yudhoyono and his inner circle.

Jakarta recalled its ambassador from Canberra and suspended cooperation in several areas over the incident, including efforts to stop people-smuggling boats reaching Australia.

Australia’s military-led efforts to turn back asylum-seeker boats also angered Indonesia, with tensions growing last year after its navy admitted entering the Southeast Asian nation’s territorial waters.

With this in mind, Abbott was careful with his words, insisting "I don’t want to make a difficult situation worse by offering gratuitous reflections on different aspects of the way this matter has been handled in recent days and week".

"As for President Widodo, look, he’s a new president, his election was attended with great promise," he said.

"I regard myself as a friend of Indonesia, I think the vast majority of Australians regard themselves as friends of Indonesia.

"My hope is that this presidency is a successful one and while this is a dark moment in the relationship I am confident that the relationship will be restored for the great benefit of both our countries."