Devi Asmarani, Jakarta – Two top separatist leaders in Indonesia's Papua and Aceh provinces have been killed in the last three months, raising suspicions that the Indonesian government is out to cripple the separatist movements by targeting their leaders, even as it promises to negotiate with them.

Tuesday's killing of Free Aceh Movement (GAM) military commander Abdullah Syafei, which followed the mysterious assassination of Papuan independence leader Theys Eluay in November, has reinforced suspicions that Jakarta's offers of reconciliation with secessionists were mere rhetoric.

Analysts doubt the killings would end bloody tension in the two resource-rich provinces, and would only raise distrust of the central government.

The Aceh rebel leader was shot dead by Army troops in a raid at his jungle base in Pidie, Aceh, while the Papuan leader was found dead in his overturned car on his way back from a visit to an army base.

Police has said its investigation showed the involvement of members of the Army's Special Command (Kopassus) in Theys's murder, but admitted it had no authority to investigate Kopassus members.

Human-rights activists said the Papuan leader's murder was part of a strategy to target local leaders. Before he died, Theys had rejected a Bill on Special Autonomy for Papua, saying the process of drafting the Bill did not involve enough local figures.

In Aceh, unidentified gunmen had killed several local intellectuals and politicians known for promoting democratic solutions to the secessionist problem there.

But Syafei's death reflected a different urgency because of its timing. The Army has said its troops stumbled upon the rebel commander and shot him during a regular tour of duty, but observers think they have intentionally killed him for political motives.

With the granting of its new special autonomy status, Aceh is set to hold province-wide elections of leaders on the regency and township levels by October.

Observers said Jakarta might see this as a potential trigger for major political tension, and it had an interest in preventing supporters of the Free Aceh Movement from running for local office. "The message of the killing is that local politicians must stick with Jakarta," said human-rights activist Munir.

The more imminent objective perhaps is the revival of a provincial military command in Aceh to tighten security grip in the province. The Army yesterday said it would set up Aceh's military command next week.

Mr Nashir Jamil of the Aceh provincial legislature said: "People here suspect that Syafei was killed to smoothen the way for the new military command." Such a military command would further erode Jakarta's credibility in Aceh, he said.