Chris McCall, Jakarta – Aceh refused to abandon its hopes for peace yesterday as a much-desired truce finally took effect under the shadow of an assassination in Malaysia.

Accusations and counter-accusations soon flew over the gunning down of dissident rebel leader Teuku Don Zulfahri in a Kuala Lumpur restaurant. Malaysian police concluded the killing was politically motivated.

Leading Acehnese still expressed hope that neither his killing nor a spate of other violence in the run-up to the truce would derail it. Thousands turned out at Banda Aceh's main Baiturrahman mosque at Friday prayers, dominated, as ever, by hopes for an end to the war.

Zulfahri headed a dissident wing within the Free Aceh rebel movement, also known as GAM, leading to suggestions he fell victim to an internal power struggle.

The rebels strongly denied this, pointing the finger at Indonesian military intelligence.

Zulfahri did not recognise the leadership of exiled rebel chief Hasan Tiro, a controversial figure who many Acehnese distrust. Zulfahri initially rejected the historic deal signed in Geneva on May 12 by associates of Tiro, pointing out its weaknesses. But he later softened his stance and backed it as a first stage to something more concrete. He hoped to see independence by 2004.

Rebel spokesman Ismail Sahputra said Indonesian military intelligence had previously abducted several Free Aceh leaders from Malaysia. "They always make operations in Malaysia against Acehnese," said Sahputra, who is from the movement's mainstream. "We had different ideas but we didn't want to kill him. We feel very sad in Aceh. The Acehnese lost a good man and a valued asset. We hope the police can find out who killed him."

Indonesian military officials could not be contacted for comment on Sahputra's claim. Few independent analysts dared to speculate on the motive for the killing in the secretive and factionalised world of the Aceh conflict, nor why it happened a few hours before the start of the truce, officially termed a "humanitarian pause".

Nevertheless, the truce went ahead and early reports were good. A rebel delegation was staying at a major city hotel and appeared to be secure there. During the morning, details of joint committees between the Government and the rebels on security and humanitarian action were released in Banda Aceh amid widespread optimism.

"It was a very impressive meeting," said Mr Saifuddin Bantasyam, executive director of Care Human Rights Forum in the capital.

At least 30 people were killed in violence between the signing of the accord in Geneva and the day the truce took effect, with another 14 missing. A series of new acts of violence were reported in the last few hours before the truce took effect at midnight. Apart from the killing of Zulfahri in Malaysia, thousands of villagers were reported on the move in Pidie district amid sweeping operations by Indonesian security forces hunting for rebels. Explosions rocked the capital until late Thursday but calm returned later.

Human rights monitors said it may not have been realistic to expect the violence to stop so quickly after a war which has lasted more than a decade and killed thousands. Hundreds, mostly civilians, have been killed this year alone amid a government-sanctioned crackdown on the rebels.