Indonesia has vowed to crush the separatists
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Indonesian troops have been stepping up their operations against separatist rebels in Aceh province.
The BBC's Orlando de Guzman said that in one incident, at least eight villagers were shot dead in the eastern Bireun area.
He said he entered the village of Mapa Mamplam as Indonesian forces were leaving. He saw the bodies of four men with bullet wounds in the back of their heads.
Eyewitnesses said they, and about four others, had been lined up and shot by the armed forces.
In another incident in the same area, a spokesman for the rebel Free Aceh Movement (Gam) told the Associated Press that 13 people, including 10 civilians, had been killed in the village of Cotrabu.
The military confirmed that an operation was under way in the area, but gave no details.
Foreign Ministry spokesman Marty Natalegawa told the BBC's East Asia Today programme that the Mapa Mamplam incident was "stories" aimed at discrediting Jakarta.
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Military forces in Aceh
Gam fighters: 5,000
Indonesian troops: 28,000
Indonesian regular police: 8,000
Indonesian paramilitary police: 2,000
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Indonesia's security operation in the province began on Monday after talks with rebel negotiators broke down, shattering a five-month-old peace deal that had raised hopes of ending 26 years of violence.
The government declared martial law and announced an all-out military offensive against Gam.
More than 150 schools have been burnt down in the province, with each side blaming the other for the destruction.
Officials say the education of tens of thousands of children is being disrupted.
Media clampdown
More troops were parachuted into the province as Indonesia's military chief, General Endriartono Sutarto, urged his forces to "hunt down and exterminate" the separatists.
"Chase them, destroy Gam," said General Sutarto.
"Don't talk about it, just finish them off."
Our correspondent says the Kopassus forces he met leaving Mapa Mamplam claimed there had been a gunfight, but villagers denied there was any exchange of fire.
Fifty schools have been torched in one district alone
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One man in the village said he had beaten up by Indonesian troops. He said he had been told: "We already killed 10 rats over there."
The Foreign Ministry spokesman said Gam was burning homes, but that that was not being condemned by the media.
"We are sick and tired... of people only pointing to situations allegedly committed by the Indonesian Government when similar - not similar - atrocities committed by the Gam are left untouched," he said.
Meanwhile, the Indonesian military governor in Aceh has ordered a clampdown on media reporting in order to deny separatist rebels a platform.
"We will bring a halt to the news from the spokesmen of Gam because they are turning the facts upside down," said Major General Endang Suwarya.
Schools targeted
The arson attacks on local schools have spread terror among Acehnese civilians.
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ACEH PROVINCE
Located on the northern tip of Sumatra island
Population of 4.3m people
Rich fuel resources, including oil and natural
gas
Home to conservative Islam - last year, Sharia law was introduced
Gam rebels are fighting for an independent state
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"We all cried when we realised the school has been reduced to ashes. Why should anyone attack a school?" a young mother in the provincial capital Banda Aceh told
Reuters news agency.
In the district of Bireun alone, more than 50 schools have been burned down.
There is no independent confirmation of who carried out the raids.
Military balance
There are 28,000 Indonesian soldiers in Aceh, confronting 5,000 Gam fighters.
Correspondents say the rebels' strongest defence is their ability to melt into the heavy forest - and into the local population.
"This war definitely can't be won in weeks like the US did in Iraq," senior military spokesman Lieutenant Colonel Achmad Yani Basuki told Reuters news agency.
He described the fighting as "of a sporadic nature. Sometimes we can hit them, but later they run away".
Acehnese resentment against Jakarta's rule has been fuelled by abuses by the Indonesian military, and a feeling that the government is exploiting the region's resources.
The failed peace deal, signed in December, offered Aceh an autonomous government by 2004, which would have been allowed to keep 70% of the revenue generated from the province's rich oil reserves.