(Transcript from World News Australia Radio)
The President says the relationship between the two nations is sound but insists any ethics agreement must be signed before relations can be fully normalised.
Prime Minister Tony Abbott has welcomed the statement but says he'll take some time to reflect on its contents.
But as Amanda Cavill reports the fall-out from the spying scandal is still having repercussions across the Asia Pacific region.
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The Indonesian response is to a letter from Tony Abbott, attempting to put an end to the diplomatic crisis over revelations that Australia tapped the mobile phones of President Yudhoyono, his wife and eight senior cabinet ministers
President Yudhoyono says Tony Abbott has promised never to do anything that will disadvantage Indonesia or damage relations.
But he says Indonesia's cooperation on things like people-smuggling remains suspended until the Mr Abbott signs up to behaviour protocols for all future dealings with Indonesia.
Mr Abbott says he's keen for a quick resolution to the diplomatic row on a strong and lasting basis.
"I am going to reflect on the statement over the next day or so and then we'll be responding more fully but my objective, as always, is to have the strongest possible relationship with Indonesia. All in all Indonesia is Australia's most important relationship. President Yudhoyono has been a great President of Indonesia. He's been a very good friend of Australia and I look forward to continuing to work together with him to ensure we bring something positive out of the difficulties of the last week or so."
President Yudhoyono says he will assign either Foreign Minister Marty Natalegawa or a special envoy to handle negotiations with Australia on the code of conduct, but insists it must be signed by himself and Mr Abbott at a formal and public ceremony.
He says the code of ethics must address the phone-tapping issue, saying he would personally inspect the draft document to ensure it meets Indonesia's expectations in addressing the 2009 incidents.
However, in a clear indication that it could be business as usual quite soon, the Indonesian President has spoken warmly about bilateral ties between Australia and Indonesia.
"The relationship between the two peoples, the people of Indonesia and Australia, is actually going well and it must be maintained."
But while tensions with Indonesia appear to be easing, the spying leaks are causing problems for other countries in the region.
President Yudhoyono says he wants to know about the reported involvement of Singapore and South Korea in the spying.
"Allegations against two countries, namely Singapore, a close friend and neighbour and fellow ASEAN country, and South Korea, one of Indonesia's good friends. They have reportedly helped Australia and America in the interception of communications under the sea in Asia and other regions, although not specifically mentioning Indonesia. I have instructed our foreign minister to ask for an explanation from the countries' envoys."
Malaysia too wants answers.
Malaysia summoned the heads of the United States and Australian missions earlier this month to protest over reports that a vast US-led surveillance network included a listening post in America's Malaysian embassy.
And just this week Malaysia's government summoned Singapore's High Commissioner for talks over reports Singapore helps Western intelligence agencies spy on the region.
Malaysia's multimedia and communication minister, Ahmad Shabery Cheek, says it cannot be allowed to happen.
"Of course, we cannot tolerate any form of spying, especially among those supposed to be friendly nations. I'm not referring to anybody in this case, unless you come up with the proper evidence and proof. Whether it is our neighbour or supposed to be our friendly countries and so on."
Papua New Guinea is also unhappy about the spying allegations.
PNG Prime Minister Peter O'Neill says he has instructed Foreign Affairs Minister Rimbink Pato to summon the Australian High Commissioner to PNG, Deborah Stokes, to provide an explanation.
"I've advised the minister that he will also bring this matter up next month at the ministerial forum; that there is a firm agreement between the two countries that there will be no intelligence-gathering between the two countries from here onwards. So that agreement must be firmed up and agreed to."
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