Indonesian soldiers have been routinely torturing suspected Acehnese rebel prisoners, according to US-based group Human Rights Watch.
The Indonesian military launched an offensive in Aceh in May 2003
Detainees are often beaten, burned with cigarettes and even subjected to electric shocks, HRW said in a report.
Military officials deny the claims, which were based on interviews with 35 suspected rebels in Indonesian jails.
Jakarta launched a massive operation against Acehnese separatists in the troubled province in May 2003.
A year later martial law was replaced with a state of civil emergency, but the conflict has continued.
According to official figures, more than 2,000 rebels from the Free Aceh Movement have been killed since the campaign began, but rights groups claim many of the dead were ordinary civilians.
The 50-page HRW report contains graphic accounts of sustained physical and mental abuse.
"I was beaten for three days and three nights ... and we were shocked with electric current," a 16-year-old detainee is quoted as
The report claims such abuses are far from uncommon.
Another prisoner is quoted as saying: "For three days we slept standing up, naked."
In many cases, HRW alleges the torture was used to extract confessions from suspected rebel sympathisers.
"Many of the prisoners told us that they had confessed solely to stop the torture," Sam Zarifi, deputy director of the New York-based rights watchdog, told the BBC.
Hundreds of people in Aceh have been convicted of treason in trials which HRW says fail to meet international standards.
The report concluded that "the scale of torture... makes it clear that these are systemic failures".
"As long as Aceh remains closed to independent scrutiny, these abuses are likely to
continue," it said.
The troubled province has been effectively closed to independent observers and journalists since the government decided to launch its offensive over a year ago.
Aceh military spokesman Lieutenant Colonel Asep denied the HRW allegations.
He told the BBC that many suspects had voluntarily surrendered to the authorities because they knew they would be well treated.
Several soldiers have already been jailed for their treatment of prisoners in Aceh, and senior military officials insist they will not tolerate human rights abuses.
"These human rights organisations always try to discredit us," Mr Sapari said. "Let them provide proof and we'll try to investigate it."
The HRW report highlights the challenges facing Indonesia's next president, former military general Susilo Bambang Yudhoyono, who promised during his election campaign that the resolution of the Aceh conflict was a top priority.
HRW called on Mr Yudhoyono to address the allegations in its report.