Prime Minister Tony Abbott says his statement on Monday linking Australia's tsunami relief contribution with calls for clemency for Andrew Chan and Myuran Sukumaran, was a "reminder" to Indonesia, and not a threat.

Mr Abbott said Australia had helped Indonesia in the past and hoped it would reciprocate, in comments that an Indonesian foreign ministry spokesman interpreted as threatening.

But Mr Abbott said On Tuesday that he was "pointing out the depth of the friendship" between the two countries.

"It was a reminder of the facts, of the depth and strength of the relationship between Australia and Indonesia, and I want that relationship to grow stronger, stronger in the weeks and months ahead," he said.

Indonesia has delayed transferring the Bali Nine pair from Bali to the island where they are due to be executed for their role in a drug-smuggling ring.

The Prime Minister said he was focused on what he "can best do to ensure that these executions don't go ahead".

"The focus has got to be ensuring that we appeal to the better angels of our natures, the focus has got to be letting Indonesia know that it is in their best interests and in accordance with their best values," he said.

Indonesian foreign ministry spokesman Armanatha Nasir warned that threats were not part of diplomatic language.

"No-one responds well to threats," he said.

"OK, it will be difficult for me or for Indonesia to see that any fallout in a bilateral relationship only affects one country.

"I hope the statement made does not reflect the true colours of Australians."

A leading Indonesian commentator has warned that Mr Abbott's attempts to save the lives of Chan and Sukumaran could further strain relations between the countries.

Pierre Marthinus from the Jakarta think tank the Marthinus Academy said Indonesians would not take kindly to the suggestion, given their overall support for capital punishment.

"This is [a] moral argument," he said.

"And we have seen the Australian public and the Australian Government giving out three major moral arguments and I don't think that they have actually resonated that well.

"If the [Indonesian] government decides to do the same I think it might even bring bilateral relations to a new low.

"I mean it's really, really bad right now."