Foreign Minister Julie Bishop says the Prime Minister's decision to link aid funding with the clemency bid for two Australians on death row was not seen as helpful in Jakarta.

Last week Tony Abbott urged Indonesia to remember the contribution Australia made towards the Boxing Day tsunami relief effort and spare the lives of Andrew Chan and Myuran Sukumaran.

Indonesia's foreign ministry reacted angrily and said the remarks were "threats" that were not part of diplomatic language.

Ms Bishop said the comments were viewed as unhelpful in Indonesia.

"It was seen in that way in Indonesia, and that's why I spoke to vice president [Jusuf] Kalla to make it quite clear that the Prime Minister did not intend to link it in an unhelpful way," she said.

"What he was pointing out was that Australia has always been a friend of Indonesia, we are there when Indonesia needs us.

"Vice president Kalla accepted that that's the way the words should be taken."

Pressed further as to whether she personally acknowledged it was seen as unhelpful, Ms Bishop said: "Well, that's how it was reported in the press."

The Foreign Minister said Chan and Sukumaran's lawyers were due to appear in court today and plan to seek to have the pair's clemency pleas reviewed.

Ms Bishop said the Federal Government was continuing to make representations on their behalf "at every level, in every department".

"I'm aware of Australian businesses who operate in Indonesia who are also making representations with government contacts that they have," she said.

"We're not leaving any stone unturned in our efforts to seek clemency for these two Australian citizens."