Indonesia's Susilo Bambang Yudhoyono is taking-on one of the toughest problems of his presidency – the long-running separatist conflicts in Aceh and Papua. Against his proposed reforms are many of the Parliament's major parties, which can block legislation; the Indonesian armed forces, and the people of both provinces, who need something more tangible than promises.

Presenter/Interviewer: Kathy Leverett

Speakers: S.P. Harish, Associate Research Fellow at the Institute of Defence and Strategic Studies, in Singapore.

Harish: So he basically has an opportunity to correct those wrongs and essentially act to bring these conflicts to a negotiated settlement, or at least to stop the violence that's been going on for so many years.

Leverett: He also took a stand more or less immediately didn't he in campaigning, saying that he would have a different policy on those two regions?

Harish: Yes. Yudhoyono has always been one of the doves in the Megawati government, even when you look at the negotiations with GAM over Aceh, Yudhoyono was by far the one who was pushing for a negotiated settlement, whereas the hawks in the Megawati government were more for the military option. Now with Yudhoyono as president, I think he will play a more significant personal role in ensuring that these two conflicts will be resolved.

Leverett: He's promised a safer and more prosperous Aceh. How is he going to do that?

Harish: In my opinion Yudhoyono's strategy is going to be in two ways. He's made it clear that autonomy for Aceh and Papua and amnesty for rebels especially in Aceh will be the maximum that he will be willing to concede. Anything further is not acceptable; any kind of referendum on the secession from Indonesian state is again not acceptable. In my opinion I think his strategy will be two-pronged. On one side he will seek to isolate the terrorist organisation GAM from the actual civilian population in Aceh.

In my opinion he will propose to do so by ensuring that autonomy, the special autonomy package that's been approved for Aceh, will actually be implemented and he will not hesitate to take a military operation against GAM. Of course he will always keep the negotiated settlement open in the sense that he will say, you are almost always welcome to come back to the table as long as you do it within the framework of autonomy, and don't insist on independence.

Leverett: Now he is facing some problems in trying to implement these fairly ambitious steps. What would you say are the biggest obstacles for him?

Harish: You are most correct, especially over the appointment of the military chief, we already see a great deal of differences between him and the Parliament. This is actually very crucial, especially in the case of Aceh, because the existing TNI chief Sutarto, and the incumbent or Megawati's choice of incumbent Ryacudu, they both had very important roles to play over the Aceh conflict. And I believe that Yudhoyono by backing Sutarto for the position, or in other words not accepting his resignation, will play a great role in how the Aceh conflict shapes. And especially if he in the coming few days, weeks we see who is going to be the next TNI chief, it will decide the way the Aceh conflict and the Papua conflict will go. If Yudhoyono gets his way I think we will be able to see more progress in the resolution of these conflicts.

Leverett: The human rights abuses by the TNI in Aceh and Papua have left deep scars. What can Yudhoyono do about that?

Harish: In my opinion I think Yudhoyono must be able to convince the people of Aceh and even the international community that every single human rights abuse will be investigated impartially and those responsible will be brought to a very speedy, transparent and open trial. This may not completely heal those scars, it's not possible to do it overnight, but it will definitely go some way in restoring some kind of trust between the Acehnese people and the Indonesian government.