In a phone conversation with Prime Minister Tony Abbott, Mr Yudhoyono affirmed that he hoped a code of conduct between the two countries could be finalised by August at the latest.
The document is the key to normalising relations between the two countries in the wake of spying revelations, asylum boat turn-backs and the withdrawal of Indonesia's ambassador.
According to the presidential press release, both leaders hope the agreement can be resolved immediately so that the bilateral relationship can enter a new phase.
Progress may be helped with a possible visit by Mr Abbott to Jakarta next month, an idea that Mr Yudhoyono says he welcomes and officials are now working on.
Mr Abbott had been due to visit Bali this week, but the ABC understands the trip was sunk by another boat turn-back.
Earlier this week the Indonesian navy released information based on its questioning of the crew of a boat who say they were turned back by Australian ships and also had three extra people placed on board.
Speaking at a leader’s summit in Bali, foreign minister Marty Natalegawa said the information that people were put on the boat by Australian authorities was yet to be confirmed.
“I am informed that apart from the apparently original 18 asylum seekers who were in the original two boats, apparently some additional three individuals were added to the boat that was forced back to Indonesia,” he said.
“So this is - if confirmed - obviously this is a very serious development.
“As I said from the beginning, we are risking a slippery slope in the facilitation of Australia's government for these individuals to be forced back to Indonesia.”
The director of the Australian National University’s Asia Pacific College of Diplomacy, William Maley, believes Australian criminal law could have been breached if the extra passengers had been in Australia’s jurisdiction.
“It actually raises the question of whether [those] involved in this particular exercise have committed the offence of people smuggling.
“Because, under the Australian criminal code division 73, there’s a provision which says that a person is guilty of an offence of people smuggling if that person organises or facilitates the entry of another person into a foreign country and the entry does not comply with requirements under that country’s law for entry.
"There may be a crucial distinction between on the one hand simply pushing back a boat which has appeared at the Australian maritime border, and on the other hand taking people who have been within Australian jurisdiction and placing them on a boat and sending them back.
“Because, arguably, the latter falls within the definition of people smuggling and there it might well be that those at sea, and those who have been involved in organising or facilitating that activity, which could of course go right up to the top level of the government, have committed a criminal offence.”
Professor Maley says Dr Natalegawa’s comments reflect Indonesia’s belief and anger that Australia’s relationship with its near neighbour runs second to domestic politics.
Labor and the Greens are maintaining the pressure on the Prime Minister to publicly elaborate on why he did not go to this week's conference in Bali.
The Greens also want Mr Abbott to say if and when he knew extra passengers were allegedly put onto an asylum seeker boat turned back to Indonesia over the weekend.
Opposition foreign affairs spokeswoman Tanya Plibersek does not accept that budget preparations prevented Mr Abbott from attending the Bali conference.
“We’re talking about a two-day round trip, telephones do work in Indonesia. I would have thought that the budget would be at such a developed stage by now that the Prime Minister could very safely have [been] out of contact for the four or five hours that he was on the plane,” she said.