Human Rights Watch went to Malaysia to interview individuals who say they fled the Indonesian province of Aceh because of the fighting.
More than 85 interviews with Acehnese were conducted in October and November 2003.
Here are the accounts of some of those interviewed:
Man from central Aceh who arrived in Malaysia in August
"I left Aceh because there is daily fighting and gunfire between the TNI (Indonesian military) and Gam all over Aceh. I can hear it from my village.
"So many things have happened. My friends have been beaten by the military. Many have been threatened. I cannot live in Aceh anymore. The trauma is too much, wondering if I am going to live or die."
A 25-year-old man who left Aceh a week after martial law was declared in May
"They're trigger happy, whether we do anything wrong or not. They kill us like ants.
"The soldiers are afraid to go into the mountains. From day one there was a new feeling, with military posts every two kilometres."
Man who left Aceh in October
"Our friends are dying as a result of the conflict. The TNI are looking for Gam. If Gam is not found they attack the community. The TNI would often enter the village.
"If we don't know where Gam is we are beaten. I was beaten twice... there has been no Gam in my village since martial law started."
Man who left north Aceh in June
"In Aceh the TNI suspect all young men of being Gam. Every day in Aceh I have to report at the TNI office so they can check that I have not left to go and join Gam. The office is in my village, but only since martial law started."
A man from north Aceh recounting an incident from May
"I saw one of the soldiers handcuff the ankles of this man, and then another soldier held him by his feet and swung him against a tree. The soldier did this many times so that the man's head was hitting the tree.
"His brains were coming out of his head, until he was dead. And then the corpse was put on the street and another soldier shot many times into the corpse.
"It was like his arm turned into raw meat. His body was destroyed."
A man talking about an incident one week after martial law was declared in May
"My older brother - he's just a civilian - was shot. Soldiers came into the village looking for Gam. There weren't any so they shot villagers instead.
"My brother was shot at our house. At 0600 he got up to wash before prayers. He went outside and they shot him immediately."
22-year-old man from Pidie
"They made me lie down, and two marines stood on my hands while one stepped on my neck. I can't remember how many times. They did it until I passed out.
"Then they threw water on me to wake me up and I was kicked again. They asked me, 'Who in the village is Gam?' They tried to force me to identify them, but there weren't any to tell them."