Lhokseumawe – A regional military commander in troubled Aceh province has defended the army's shooting of protesters, as officials said Wednesday the death toll had risen to 31.

Colonel Johny Wahab was quoted by the Kompas daily Wednesday as saying the protestors action threatened the entire town of Lhokseumawe, the main town in the North Aceh district on Sumatra island.

Wahab, who was out of town when Monday's shooting took place, said the military headquarters the demonstrators were heading for housed several missiles which could have been used to blow up the town.

Lieutenant Colonel Nurdin Sulistyo of the military command based in Medan, in the neighbouring province of North Sumatra, said the protesters had to be stopped. "We deplore the incident but because people ... wanted to enter the headquarters of the military missile detachment, this had to be prevented because that place is dangerous, full of missiles," he said.

Soldiers opened fire on more than 2,000 protesters blocking a main junction 10 kilometres west of Lhokseumawe. The protesters encountered the soldiers as they tried to march to a military headquarters in Lhokseumawe from the village of Krueng Geukueh, 15 kilometres away, to protest against military violence at another village, a local journalist said.

T.S. Sani, from the North Aceh district authorities' fact-finding team, told AFP said that by midnight Tuesday "we had found a total of 31 bodies including that of one man nobody has been able to identify so far." There were 91 seriously injured in hospital and another 23 injured people had been taken home by relatives after treatment, Sani said.

A local Red Cross representative, Mauludi, said his death toll matched that of the fact-finding committee, but his records showed 100 seriously injured "all of gunshots" and 100 others were treated for light injuries.

"We have not yet completed registering those victims, dead or wounded, who have been taken away by their families," Sani said. "This will need time to process, so that we can obtain authentic and accountable data." Mauludi said all the dead had now been buried.

Indonesia's armed forces chief General Wiranto on Tuesday said he regretted the shooting and promised an investigation. The National Commission on Human Rights will send three people to Lhokseumawe on Monday, Commission member and former national police chief Kusparmono Irsan told AFP.

"We are currently gathering data from Jakarta in preparation for the fact finding visit to Aceh," Irsan said. The military has said the first shots were fired from the crowd and soldiers returned fire in self-defence.

But a local journalist said troops fired at the crowd after some of the protesters began to pelt them with stones. The crowd had intended to protest over violence by soldiers at nearby Cot Murung, during a house search by troops.

The soldiers were looking for a sergeant they said had gone missing after he was caught by villagers during a rally of the Aceh Merdeka (Free Aceh) separatist movement on Saturday.

Villagers accused the soldier of infiltrating the rally while the military said he was visiting a relative. The Aceh Merdeka (Free Aceh) has been fighting for an Islamic state in Aceh since the 1970s.