John Aglionby, Jakarta – Hundreds of thousands of people gathered yesterday in and around the capital of Aceh province for a huge two-day independence rally, despite scores of killings by security forces trying to frighten off demonstrators.

As more than 300,000 protesters gathered, President Abdurrahman Wahid warned his military not to use violence to try to stop the rally. "I will not let Acehnese ... be shot," the official Antara news agency quoted him as saying. "I'm in charge of the military and police. Do they think I'm afraid to fire them?"

Mr Wahid said any further violence could ruin the truce between the Government and the separatist Free Aceh Movement that took effect in June and has been extended until January.

Human rights groups said at least 21 people had been killed by Indonesian troops over the past two days, many at roadblocks as they tried to travel to the provincial capital, Banda Aceh.

A co-ordinator of human rights groups in Aceh, Mr Faisal Hadi, said another 101 people had been injured in incidents in the province, on Sumatra's northern tip. "It is clear the police and army were prepared to do anything to stop people reaching Banda Aceh for the rally."

Some of the deaths happened when convoys of trucks and cars refused to turn round at police roadblocks, he said. Others were shot when they tried to reach the city by boat. "Police opened fire into the crowds while they were at sea and also trying to dock. There was no way they could miss."

Police admitted shooting 13 people dead, "in self-defence", but human rights organisations monitoring events said the final death toll could be more than 40 once their staff had checked reports from remote areas.