Security fears in the first post-agreement phase focused on GAM and the military. But demobilisation and disarmament under the Helsinki Memorandum of Understanding (MoU) proceeded smoothly, largely because of clear deadlines, good faith on both sides, and the robust mandate of the Aceh Monitoring Mission (AMM). A Commission on Security Arrangements (COSA), comprising representatives of GAM and the armed forces and chaired by the head of AMM, provided an effective forum for discussion of security concerns.
The big problem in this first phase, and one that would continue to haunt the post-agreement period, was reintegration. The initial reintegration programme was based on the idea that GAM would turn over a list of 3000 names as per the terms of the MoU and financial packets would be handed out accordingly. GAM officials resisted releasing names, ostensibly on security grounds, concerned that they could become a hit list in the event of future conflict. That was a genuine fear, given its experience with past ceasefires, but the real problem was how to divide up the money among a much larger population. The solution was to give it to commanders and hope they divided it equitably. Inevitably, it did not work and became a new source of conflict.
A further problem during the first eighteen months was the functioning of the Aceh Reintegration Board (BRA). The poorly planned and even more poorly administered BRA generated enormous problems for itself at the outset by soliciting proposals for livelihood projects from "conflict victims". When this approach resulted in a staggering volume of proposals, the BRA changed tack and proposed a community-led approach channelled through the World Bank, causing considerable anger.
A further sensitivity associated with the BRA was the government's de facto acknowledgement of the existence of militias.
To avoid accusations that it was rewarding rebels, the agency decided to give Rp.10 million (about US$1000) to 6500 militia members, otherwise known as "anti-separatist fronts" or "homeland defenders" (Pembela Tanah Air, PETA). Inclusion of militia members in the reintegration programme was probably a necessary step to avoid tensions. The Indonesian military had always denied any role in creating these fronts, but in the end, it was the district military commands that provided the names of those eligible for funding. While fears that militias, backed by intelligence operatives, could become election spoilers did not materialise, the fault line between ex-rebels and loyalists remained, particularly in Central Aceh and Bener Meriah districts. This tension resurfaced dramatically in early 2008 when five members of the KPA – (Komite Peralihan Aceh, Aceh Transition Committee, the new name for the old GAM military structure) were killed in the worst act of violence since the peace agreement was signed.
Intra-GAM problems had been brewing for some time between the old guard, based in Sweden and led by Malik Mahmud, who had headed the negotiating team in Helsinki, and the younger field-based faction, led by Irwandi Yusuf. The rift initially had few security implications, but an attack in November 2006 on Humam Hamid, the old guard's candidate for governor, raised concerns about more violence to come, particularly in Bireuen district, where the camps were locked in bitter contention.
If KPA vs militias was one source of tension and GAM factionalism another, a third was that between Aceh and the central government, as illustrated by the differences over the Law on the Governing of Aceh (LoGA). The self-government promised to Aceh in Helsinki was considerably diluted in the law, and what GAM leaders view as the unimplemented provisions of the Helsinki agreement could become the basis for resumption of conflict in the future.
No serious security problems arose during the December 2006 elections in which Acehnese voters decisively chose a GAM governor and GAM candidates in seven out of nineteen races for district heads (bupati). In the general euphoria over the results, concerns over extortion and intimidation on the part of some KPA members went largely unnoticed.
Shortly after the elections, the AMM left Aceh, leaving in its wake no agency with the same authority to resolve disputes and defuse conflict. A new body called the Communications and Coordination Forum (Forum Koordinasi dan Komunikasi , FKK), on which KPA and Indonesian military officers both sit, was set up in April 2007 as part of the Aceh desk under the Coordinating Ministry of Politics, Law and Security but its mandate was narrower. It has been a useful forum when security incidents occur, such as the March 2008 attack in Central Aceh described below. But it is less effective for resolving struggles over administrative authority between Aceh and the central government.