Indonesia has accepted an explanation from Australian Foreign Minister Julie Bishop about comments linking tsunami aid to the fate of two Australians on death row.

Vice president Jusuf Kalla confirmed he spoke to Ms Bishop on Thursday by phone after Prime Minister Tony Abbott earlier this week linked Australia’s tsunami relief contribution with calls for clemency for drug smugglers Andrew Chan and Myuran Sukumaran.

• Racist Chelsea fans should be punished: victim
• Boat carrying Sri Lankan nationals intercepted
• Indonesia hits back at Abbott over diplomatic ‘threats’

Indonesia’s foreign ministry reacted angrily and said the remarks were “threats” that were not part of diplomatic language.

But Mr Kalla said Ms Bishop had explained the comments and “expressed regret in regards to the misunderstanding”.

He also said Ms Bishop told him Australia wanted to continue its long years of cooperation with Indonesia, which included assisting in the recovery from the 2004 tsunami.

Mr Kalla said Australia also wanted to help Indonesia fight its illegal drugs problem.

Ms Bishop confirmed the conversation took place.

“I have made it quite clear that the Prime Minister was simply illustrating the point that Australia has been and remains a supporter, a close friend of Indonesia,” she said.

“Certainly these comments were not any attempt to threaten Indonesia.”

Ms Bishop said she was working to stop the executions of Chan and Sukumaran.

“I’m continuing to work at every level in the Indonesian government, our diplomats in Jakarta and in Bali,” she said.

“[I’m] working with the families and also working with the Indonesian authorities to continue to press our case that there should be a stay of execution and that their clemency pleas should be reconsidered.”

Transfer meeting concludes without a date

Indonesian government officials are pressing ahead with organising the transfer of prisoners for the executions which were due to take place this month, but were delayed by logistical issues and the need to check the mental health of a Brazilian man.

On Friday attorney-general Muhammad Prasetyo said a timeline for the transfer and executions of Chan and Sukamaran had not been finalised.

“We have not set a time yet,” he said.

“All preparation needs to be finalised first, and we need to make a coordination with all stakeholders who will be involved in the execution.”

When asked by a journalist why Australia was protesting “so hard”, Mr Prasetyo said “that is normal”.

“When we have our citizen also on death row, we would have [done] the same. That’s why we respect and respond on their request or concerns,” he said.

A preliminary hearing is due in the administrative court in East Jakarta next Tuesday, with Chan and Sukumaran’s lawyers attempting to have a full hearing granted so they can challenge the president’s decision to deny them clemency.

Mr Prasetyo said while he acknowledged the right for Chan and Sukamaran’s legal team to continue its efforts to stall the process, he did not agree with the argument.