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.