In heartbreaking scenes played out live on television, the families of Myuran Sukumaran and Andrew Chan have begged Indonesian President Joko Widodo to spare the lives of their loved ones, following their final goodbyes.

With the Bali nine ringleaders due to face the firing squad about midnight (3am AEST), Sukumaran's sister Brintha wailed with grief, begging for her brother's life.

"Indonesian people, show mercy. Please don't do this to my brother. Please, please Mr President, Joko Widodo, I beg you please. Please don't take my brother from me," she said.

Between anguished cries, his mother, Raji, told journalists of her last moments with her son.

"I just had to say goodbye to my son and I won't see him again," she said through tears after her return to the port of Cilacap.

"They are going to take him at midnight and shoot him.

"He is healthy and he is beautiful ... I'm asking the government please don't kill him today. Please don't hold the execution. Please don't kill my son."

Holding back tears, Chan's brother Michael said Tuesday was one of the hardest days the family would face.

"To see Andrew hold up the way he did, being dignified and courageous through these tough and dark hours.

"I saw today something that no other family should ever have to go through. Nine families  inside a prison saying goodbye to their loved ones. Kids, mothers, brothers, cousins, sisters, you name it they were all there. To walk out of there and say goodbye for the last time - it's torture. No family should have to go through it.

"There has to be a moratorium on the death penalty. No family should endure it because now the family will go through a grieving process for the rest of his life.

I hope the President somewhere in his heart can find the courage to call this off. It's not too late. It's up to him."

Late on Tuesday night, Indonesia still had not formally notified the Australian government of the impending executions as a former ambassador warned the two countries were facing their most serious rift since the East Timor crisis.

High-level ministerial meetings with Indonesia will be cancelled and senior government sources say all aspects of the diplomatic relationship are "on the table" in the fallout of the Bali nine case.

Fairfax Media has also confirmed that the Abbott government will now almost certainly withdraw Australia's ambassador.

Sukumaran's brother Chinthu said he did not have much time with Sukumaran and there were so many things to talk about. They did talk about the death penalty.

"He knows this is just a waste. He knows this is not going to solve anything. Drug taking is still going to be there. These nine people die today - tomorrow, next week, it's not going to stop anything.

"Please show mercy," he said. "Please don't let my mum and sister have to bury my brother."

Sukumaran told his family he and Andrew Chan would stay strong and look after the seven others facing death.

He was particularly concerned about Filipina maid Mary Jane Veloso, the only female in the group.

Earlier in the day, the families had arrived at the port for their last visit with Chan and Sukumaran.

It was the day Sukumaran has been painting. Paintings of hearts broken, literally and figuratively. Self-portraits of the artist with gaping black holes over his heart and lines of black blood, paintings of the life draining out of him in whooshes of thick paint. And on Tuesday, the day of final goodbyes, a portrait of a human heart.

Inscribed was "Satu hati satu rasa didalam cinta" - one heart, one feeling in love. It was signed by all nine of those on death row whose hearts will be ripped apart by bullets.

It seemed that Tuesday could not get any any worse for Sukumaran and Chan and their loved ones. But it did. At the eleventh hour the families learned that the men had been denied their choice of a spiritual counsellor who stays with the condemned until the bitter end.

As Michael Chan told Fairfax Media in an SMS: "Last bit of dignity denied."

Chan and Sukumaran had asked for Salvation Army minister David Soper and Bayside Church Senior Pastor Christie Buckingham to accompany them until their deaths .

Both are old friends, both know the men intimately and their journey over the past decade since their 2005 arrest for smuggling heroin out of Indonesia.

Both have witnessed their transformation from stupid, selfish young men to the painter and the pastor.

The reasons for the last minute denial seem inexplicable: just two days earlier the Australian Embassy had been assured it would be ok.

After frantic and frustrating negotiations throughout day, the two ministers will be allowed to return to Nusakambangan for a few hours. But they will not be permitted to comfort them in their last minutes on earth or witness their execution by firing squad.

On learning this final request had been refused the families were forced to walk the gauntlet of a frenzied media scrum.

In past days they had been driven into the ferry dock, but on Tuesday had to walk the dusty narrow road to the harbour.

The Sukumaran family became trapped inside a feverish media pack as they boarded the ferry to Nusakambangan - now referred to simply as "execution island" - for the last time.

It was impossible for them to move. Brintha Sukumaran collapsed. A wild-eyed male relative screamed in fright. Police dogs snapped and snarled at ankles. News Limited journalist Cindy Wockner was bitten on the leg.

After an eternity the family made it to the port. We could hear the anguished wails long after they disappeared from sight.

A planned press conference was cancelled.

Chan is now a pastor, and as of Monday, a married man.

He and his wife Febyanti Herewila had reportedly dreamed of setting up a community centre on Sabu Island, west of Timor, to hold music classes and provide a place for young people to play sport and learn.

Sukumaran is an artist who this year was awarded an associate degree in fine arts from Curtin University.

His legacy - the art and other classes he established at Bali's Kerobokan jail - have changed the trajectories of other prisoners' lives.

"Myu is ok. He is ready for what is to come," Sukumaran's friend and mentor Ben Quilty wrote on his Facebook page.

"But with his passing my world will take a dark plunge backwards."

Quilty said "Myu" had inadvertently brought together compassionate and forgiving people, around the world. "Together we will all ensure that compassion continues to flourish."

"Myu made terrible mistakes," Quilty said. "So did I, but his family and his friends will pay a dreadful price for his youthful self-indulgence. And so will Myu."