Lhokseumawe – Weapons are not the way to wipe out the separatist Free Aceh Movement (GAM) guerrilla army even though their leader was killed last week, says the commander of Indonesian forces in the restive province.

"To annihilate them, to finish them off, doesn't have to be done with weapons. That's not our way," Brigadier-General Djali Yusuf told AFP on Wednesday in his first interview with a foreign journalist.

Calling the separatists "our brothers", Yusuf – himself Acehnese – said the government is still appealing to them to end their struggle and has given them until February 11 to enter into dialogue.

But Yusuf, 52, said he would not compromise in his mission to preserve the unity of Indonesia. "There is no bargaining on this. Aceh is part of the Republic of Indonesia. It can't be negotiated," he said. "Although I'm a native son of Aceh, I have to be firm in carrying out my duty."

Speaking at his headquarters in this city, which is home to a giant ExxonMobil natural gas production facility, Yusuf said he has not seen any change in the behaviour of GAM despite the death in battle of their military commander Abdullah Syafii on January 22.

"It looks like the death is not going to alter their plan of operations," said Yusuf, who took command of 17,000 troops last November. He had been deputy commander since Indonesia began a military offensive last May.

GAM guerrillas have been fighting since 1976 for an independent Islamic state in a conflict which has claimed an estimated 10,000 lives. Jakarta has granted the province on the northern tip of Sumatra island greater self-rule and a much larger share of oil and gas revenues but has ruled out independence.

Rebel representatives in Aceh say they will boycott planned peace talks in Switzerland this weekend with the Indonesian government because they are still mourning Syafii. GAM's exiled leadership in Sweden has yet to announce a final decision on whether to attend the dialogue.

Yusuf, smoking a series of clove cigarettes through an elegant holder, said daily life and government activity – which had been paralysed – has started to return to normal as a result of the military operation. He said his forces have killed close to 300 GAM troops since last May and seized about 400 of their weapons, with the loss of about 50 government soldiers.

A human rights worker in the provincial capital Banda Aceh agreed the military has become more accurate in its targeting of GAM guerrillas but said most victims in the conflict are still civilians. Human Rights Watch recorded more than 1,300 deaths last year, most of them non-combatants, and the Aceh NGO's Coalition for Human Rights documented 33 civilian deaths in the first 24 days of this year.

Yusuf said there have been only seven civilian casualties during the operation since last May. The other victims are GAM members who did not have weapons, he said, adding that his troops carry special cards reminding them of their obligation to respect human rights.

Disputing GAM claims that a tracking device helped lead hundreds of Indonesian troops to Syafii's base last week, Yusuf said a team of just 20 soldiers came upon the hideout while investigating a resident's report about an armed man. "My soldiers didn't know that it was Abdullah Syafii," he said, suggesting that a larger force would have been sent if he had been forewarned of Syafii's presence.

Yusuf, a soldier for 29 years, was in Jakarta when Syafii died. He flew back to Aceh to personally check the corpse of his adversary.