The families of Andrew Chan and Myuran Sukumaran were not told they could stay with their loved ones for an extra six hours and have returned from the penal island where the prisoners are set to be executed overnight.
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A spokesman for Indonesia's Attorney-General, H. M. Prastyo, revealed earlier on Tuesday the families of the two Australians could stay on the island where their executions will take place up until 8pm (11pm AEST).
But they returned by boat about 3pm local time, unaware of the extension of time to say their final farewells.
"I just had to say goodbye to my son and I won't see him again," Sukumaran's mother Raji said through tears after her return to the port of Cilacap.
"He is healthy and he is beautiful ... Please don't kill him today, please don't kill my son."
In scenes of despair, Mrs Sukumaran and other relatives of the condemned prisoners fronted international media.
Chan's brother and Sukumaran's brother and sister also pleaded with the Indonesian President not to go ahead with the executions.
Earlier, Mr Prastyo refused to confirm the time of the executions, saying it could happen any time this week - but also said the Indonesian government would not be advising when the execution would take place at all.
The Attorney-General will only confirm the men have died after it has happened.
His spokesman, Tony Spontana, said the bodies of the two Australians would be taken to a morgue in West Jakarta, at the request of the Australian government, before they are flown home.
A local Christian pastor has yet to be found to witness Andrew Chan's execution, suggesting the delay may be for logistical reasons.
However, Fairfax Media has been told that morticians, spiritual advisers and others permitted to attend the executions are being asked to gather in Cilacap at 8pm local time tonight, ahead of their transportation to Nusakambangan Island.
In a brief statement as they disembarked at Cilacap port, Myuran Sukumaran's brother, Chinthu Sukumaran, once more pleaded for the Indonesian president Joko Widodo to intervene and spare his brother's life.
"You're ordering the murder of nine people - these are people with families that love them, they don't need to die," he told reporters.
"I ask you to please show mercy ... Myuran is at peace with what will happen, he knows he has to be strong and take care of the other people who are with him, and we know that's his focus."