A peace agreement signed last week paves the way for the creation of a human-rights court and a truth and reconciliation commission, but the government's public stance is that past crimes will not be investigated.
The two bodies will only hear cases carried out after the accord's 15 August signing date, Information Minister Sofyan Djalil said late on Tuesday, adding that the "spirit of the accord was to forgive".
The 29-year war in the oil- and gas-rich province on Sumatra island's northern tip has claimed 15,000 lives, many of them innocent villagers.
Human-rights groups accuse the military, and to a lesser extent Free Aceh Movement rebels, of widespread atrocities during the conflict, including killings, disappearances and collective punishment of civilians.
Some analysts say the government is playing a delicate balancing act aimed at appeasing the military and conservative lawmakers - many of whom are upset because the peace accord was negotiated without the approval of parliament - and could later change its stance.
The peace pact did not have the
Indonesian parliament's assent
Exiled rebel leaders who signed the pact say they are confident the proposed human-rights court and truth and reconciliation commission - which could be patterned after the one that examined the apartheid-era brutality in South Africa - will hear past crimes.
Southeast Asia project director for the International Crisis Group, Sidney Jones, noted that the last peace accord collapsed in part because the military did not withdraw its troops as demanded by the rebels.
She said the government might be trying to reassure soldiers and police - who have just started pulling out of Aceh - so that they follow through with the agreement.
Rebel spokesman, Bakhtiar Abdullah, said separatist negotiators were under the impression major atrocities would be heard by the human-rights court, while less serious abuses would come before the truth commission.
"Amnesty would be given if they appear before commission," said Abdullah by phone from Stockholm, Sweden.
"My concern is that without giving justice to the people of Aceh ... peace won't be sustained because people will take revenge"
Kontras rights group
"But it must be under international standards. If it were done by Indonesia alone, I'm afraid nothing would be achieved."
Some human rights activists, meanwhile, warn that if crimes of the past are ignored, the Acehnese may take justice into their own hands.
"My concern is that without giving justice to the people of Aceh ... peace won't be sustained because people will take revenge," said Usman Hamid, from Kontras, a rights group that has investigated abuses in the province of 4.1 million people.