Indonesia's President Joko Widodo refused clemency for the Bali nine duo facing execution without all the documentation of their cases due to the chaotic handover to his office from his predecessor.

A source familiar with the events, who asked not to be named because of the extreme sensitivity of the case, told Fairfax Media Mr Joko had little more than a list of drug offenders on death row when he made the decisions.

"Look, the current President simply takes over all pending applications of the death felons from the previous government, which the latter did not touch at all," said the source.

"And there was just a few pieces of papers listing names of people on death row. No documents attached to the lists."

The source said that the President did not have a complete understanding of the rehabilitation of Myuran Sukumaran and Andrew Chan, or documentation outlining the testimony from a former governor of Kerobokan prison.

The governor, Siswanto, testified that their transformation was genuine and had profoundly affected the penitentiary.

The two organisers of the Bali nine heroin smuggling ring have run numerous vocational education courses inside Kerobokan, counselled drug addicted inmates and raised money for medical procedures for their fellow convicts and to improve facilities in the prison.

Mr Joko was sworn in as President in October and refused the clemency of Sukumaran and Chan in December and January respectively.

His predecessor Susilo Bambang Yudhoyono had failed to consider their clemency for years and, after he left, the complete documentation for the clemency bids was not forwarded to Mr Joko's staff.

Fairfax Media understands the main list of 64 convicts on death row used by Mr Joko contained only the most scant information - names, nationality, ages when they were arrested and sentenced, the status of their legal appeals, and the province in which they are incarcerated.

The revelations that Mr Joko had been making his clemency decisions without full information comes as lawyers for the pair prepare an appeal to Jakarta's administrative court arguing the process around the clemency rejection was flawed.

They argue that the President rejected all the clemency petitions without reviewing them individually.

"Without wanting to disrupt the President's prerogative [to granting clemency], we submitted the lawsuit only due to the lack of clarity of reasons behind the President's decision to not grant pardon," said Todung Mulya Lubis, a lawyer for the pair.

After the decision on Tuesday to delay the transfer of the pair from Kerobokan to the execution island of Nusakambangan, the families and the duo's lawyers have expressed relief that they have been given more time to press their case.

However, Prime Minister Tony Abbott's comments that Indonesia should show mercy because of the $1 billion in aid provided to the country after the devastating 2004 tsunami in Aceh have not gone down well in Jakarta.

"Threats are not part of diplomatic language," said foreign affairs spokesman Arrmanatha Nasir. " And from what I know, no one responds well to threats."

Minister for Foreign Affairs Julie Bishop said earlier that the postponement of the men's transfer from Bali was a positive sign.

"While Mr Sukumaran and Mr Chan are still alive, there is always hope," she said. "We are continuing to press the case, just as Indonesia seeks clemency and seeks stays of execution for its nationals who find themselves facing the death penalty overseas."

Tim Lindsey, a professor of Asian law at Melbourne University, said the delay suggested the "headlong rush to execute has been interrupted and that is something".

"It does represent an opportunity for the government to take a breath about where it goes from here," he said.

He added the situation was becoming more difficult for Indonesia as international criticism mounted over its "blatant double standards" when it came to executions.

"The next time they have a maid facing decapitation in Saudi Arabia and they are seeking to get clemency for her, the government is going to say you haven't shown any similar mercy to those executed in your country.

"Imagine if someone was decapitated because of that - the government would be hugely criticised."

Professor Lindsey said presidential candidate General Prabowo Subianto got political mileage during last year's election campaign out of Indonesia's blood money payment to spare the life of a maid in Saudi Arabia.

"You have two populist policies colliding - execute drug smugglers and save Indonesians overseas. That is unsustainable."

A solution, he said, was to adopt the Constitutional Court recommendation that prisoners have their death sentences commuted to life imprisonment if they have been on death row for 10 years and have reformed.

The Bali nine duo have been on death row for almost 10 years over their role in the foiled attempt to smuggle 8.3 kilograms of heroin to Australia.

The head of the Bali correctional facility, the Bali police chief and the head of the Bali paramilitary unit met at Kerobokan prison on Wednesday.

The head of the Bali correctional facility, Nyoman Putra Surya Atmaja, said the police chief wanted to see the location and meet Chan and Sukumaran.

He said the brief meeting was "very relaxed" and the Australians didn't ask any questions.

"They had other things to do like meeting with family, so the meeting was very brief, maybe a minute or two. Andrew was with his family and Myuran was painting," Mr Atmaja said.

He said they were ready to hand over the prisoners but the timing was up to the Bali prosecutor's office.

Meanwhile, the lawyer for Brazilian man Rodrigo Gularte, who was convicted of smuggling 19 kilograms of cocaine in his surfboard in 2004, said the Attorney-General's office would seek a second opinion on whether his client had paranoid schizophrenia.

Ricco Akbar hopes Gularte will not be executed because he has been diagnosed with symptoms of paranoid schizophrenia.

"They will get another doctor to examine him and provide a second opinion before they decide what to do with Rodrigo."

He said it was against the law to execute a mentally ill person or a pregnant woman.

Gularte is one of the nine other prisoners slated to be killed with Chan and Sukumaran in the second round of executions to be held in Indonesia this year.

Two others among the 11 - Mary Jane Fiesta Veloso from the Philippines and Serge Areski Atlaoui from France - have both reportedly been given a reprieve to pursue legal appeals.

With Karuni Rompies and Amilia Rosa