More than 40,000 Indonesian troops have been sent to overcome the Free Aceh Movement which has been fighting for independence since 1976. The BBC's Rachel Harvey looks at the human cost of the government offensive.
Men in Aceh are questioned by Indonesian soldiers
We heard the singing as soon as we turned into the lane. We had left the cars parked near the main road, and we'd been walking for perhaps five minutes along a rutted dirt road. We were looking for a village where we had heard there had been shooting the day before.
The further we walked along the dusty track, the louder the singing became, until we reached a small crowd outside a house - mostly women and children.
We asked what was going on. It was a funeral, a mother burying her son. He had been shot dead the day before. The singing was part of the burial ritual - prayers from the Koran to send the body on its way.
The dead man's name was Fadhil. He was 20-years-old. He was a supporter of Aceh's separatist rebels, known by their Indonesian acronym, Gam.
He was on his motorbike on the lane outside when he was shot in the leg by Indonesian soldiers.
They pulled him from the bike and took him away. Later, when his mother found his body, it was covered in cuts and bruises. But it was the second gunshot which probably killed him.
He had a bullet hole in the centre of his forehead; the back of his head was missing - it had been blown away.
His mother was left to clean the body ready for burial.
"Why did they do this?" she asked me. He was a Gam member, but he wasn't armed when they shot him.
The longer we stayed in the village the more people came forward with stories to tell. An old woman with a wrinkled face pushed her way through the crowd.
A soldier conducts a house-to-house search for rebel fighters in Aceh
She told me she had arrived two days before looking for a safe place to stay. Soldiers had come to her own village. She saw six young men dragged from their houses.
The soldiers beat them with rifle butts until they fainted. She demonstrated the action for me, thrusting at the ground with her imaginary gun.
Another, younger woman, standing off to one side, began sobbing uncontrollably. She had heard we were here and wanted to know if we had any information.
She had come on a scooter and still had a black helmet perched on her head.
"Where is my brother?" she asked over and over again.
He had been taken away by the Indonesian military the day before, along with most of the other young men of the village.
Nothing had been heard from them since. Some of them probably were rebel supporters, but not all.
What we heard in this particular village sadly wasn't an isolated incident. In the first week of the Indonesian security forces operation against separatist rebels in Aceh there were many similar stories.
Harrowing accounts of beatings, intimidation and, in some cases, executions.
Most villagers we spoke to said the abuses were carried out by Indonesian soldiers. The military denies any improper behaviour but has said it will investigate, just to be sure.
One thing is certain. Unarmed young men in Aceh have been shot, at close range, sometimes in the back of the head.
And whoever carried out the killings is guilty of war crimes.