A Human Rights Watch report on Thursday said Acehnese refugees interviewed in Malaysia have revealed widespread abuses in the Indonesian province.
Aceh has been effectively closed to observers since martial law was imposed in May, when the Indonesian military moved in to crush the separatist Free Aceh Movement (GAM).
HRW said the province should immediately be opened to independent observers, journalists and humanitarian agencies.
This would serve as a deterrent to further abuses and would provide much needed humanitarian assistance to civilians affected by war.
"Every Acehnese we interviewed had a story of abuse to tell," said Brad Adams, executive director of HRW's Asia division.
"We fear that the abuses we have uncovered against the civilian population may be just the tip of the iceberg."
Witnesses told HRW about village sweeps in which civilians were killed, some while being questioned or detained and others while fleeing in fear of mistreatment.
"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"
Aceh torture witness
And victims and witnesses recounted in shocking detail how Indonesian forces appear to be targeting young men in Aceh.
"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," one young Acehnese man said.
"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."
HRW said it is concerned many Indonesian soldiers seem to presume all young men in Aceh are GAM fighters, and are targeting civilians indiscriminately.
"In case after case, soldiers have gone into Acehnese villages
and publicly executed or beat people seemingly at random," said Adams. "If the aim is to instill fear in the populace, sadly it's working."
The rights organisation has called on the Indonesian military to put an end to ongoing abuses and ensure rights violators are brought to justice.
"It is time for the Indonesian military to take its responsibilities seriously to follow international law in its conduct of war," said Adams.
"Establishing accountability for human rights abuses in Aceh and ensuring that the perpetrators are brought to justice are essential if the decades-long conflict is to be resolved. It is also necessary if Indonesia is to regain credibility with the international community."
The Aceh offensive is Indonesia's largest military campaign since the country's invasion of EastTimor in 1975.
The operation involves an estimated 30,000 troops, who are opposed by an estimated 5000 members of GAM.
Civilians have been the main
casualty of the Aceh conflict
Officially, the Indonesian government has said 1200 rebels have been killed since the offensive began in May, but observers say it is impossible to confirm any figures.
Indonesia has said military actions must be seen in the context of a "war situation", and that atrocities are also being carried out by GAM.
Officials say commanders cannot be expected to have complete control over all of their troops when they are facing a "terrorist" insurgency.
And they say they are keeping groups like Human Rights Watch out of the country because they are biased against Indonesia.