Indonesia executed seven foreign drug convicts including two Australians by firing squad Wednesday, causing Canberra to withdraw its ambassador over the "cruel" punishment.

Authorities put the seven plus a local man to death after midnight (1700 GMT Tuesday) on the high-security prison island of Nusakambangan in central Indonesia, but a Filipino was spared at the 11th hour.

"We respect Indonesia's sovereignty but we do deplore what's been done and this cannot be simply business as usual," said Australian Prime Minister Tony Abbott.

"For that reason, once all the courtesies have been extended to the Chan and Sukumaran families our ambassador will be withdrawn for consultations."

Andrew Chan and Myuran Sukumaran, ringleaders of the so-called "Bali Nine" heroin-trafficking gang, were described as reformed men after years in prison by Australian Foreign Minister Julie Bishop, who joined Abbott at a press conference in Canberra.

Australia had mounted a sustained campaign to save its citizens, who have been on death row for almost a decade, with the prime minister repeatedly appealing for them to be spared.

Australia has never recalled an ambassador over a drug execution before, but the punishments were "both cruel and unnecessary", Abbott said, necessitating the "unprecedented" move to bring back Ambassador Paul Grigson.

In a statement, the families said their sons did "all they could to make amends, helping many others" in the years since their arrests, with Sukumaran teaching fellow inmates English and art, and Chan ordained as a minister in February.

"They asked for mercy, but there was none. They were immensely grateful for all the support they received. We too, will be forever grateful."

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'Yes, yes mama will live'

The Philippine government expressed delight at the late reprieve for Mary Jane Veloso, whose case attracted emotive appeals for mercy from boxing superstar Manny Pacquiao among others.

"The Lord has answered our prayers," Foreign Affairs Department spokesman Charles Jose said, as activists holding a vigil in front of the Indonesian embassy in Manila broke into cheers and hugged each other.

Veloso was spared after someone suspected of recruiting her and tricking her into carrying drugs to Indonesia turned herself in to authorities in the Philippines.

"Miracles do come true," her mother Celia told a Philippine radio station, adding that her daughter's two young boys were awake and yelling "Yes, yes mama will live".

The other foreigners executed were one from Brazil and four from Africa.

Three of the African traffickers are confirmed as being from Nigeria. However it is not clear whether the fourth holds Ghanaian or Nigerian nationality.

The execution of the Brazilian, Rodrigo Gularte, has generated much criticism in his homeland, with his family saying he should not have faced the firing squad because he had been diagnosed with schizophrenia.

Gularte's cousin was observed leaving the port crying, accompanied by a religious counsellor.

The Brazilian government expressed its "deep dismay" at his execution and interim foreign minister Sergio Franca Danese said Brazil was "evaluating" its relationship with Indonesia after its repeated appeals for clemency were ignored.

France said it "reiterates its opposition to the death sentence in all cases and all circumstances".

A Frenchman was originally among the group to be executed but he was granted a temporary reprieve after authorities agreed to allow an outstanding legal appeal to run its course.

'Utterly reprehensible'

In Indonesian executions, convicts are led to clearings just after midnight, tied to posts and then given the option of kneeling, standing or sitting before being executed by 12-man firing squads.

President Joko Widodo has been a vocal supporter of the death penalty for drug traffickers, claiming Indonesia is facing an emergency due to rising narcotics use.

He has turned a deaf ear to appeals from the international community, led by United Nations chief Ban Ki-moon.

Amnesty International condemned the executions as "utterly reprehensible" in a statement from research director for Southeast Asia and the Pacific Rupert Abbott.

Following the executions, ambulances carried coffins away from the island where the men were put to death, with some shrouded in embroidery and others made of plain wood, according to an AFP reporter at the scene.

Australia's consul general to Bali, Majell Hind, who took custody of the bodies of Chan and Sukumaran, was seen departing the Cilacap port with other consular officials in a heavily tinted van.

Hind was tasked with delivering the news of the executions to the Chan and Sukumaran families, who are staying at a nearby hotel.