Army officials said that Teungku Jaelani, the Free Aceh Movement (GAM) governor of Central Aceh, was the most senior rebel to have been killed since Jakarta launched its fresh military offensive against the rebels in May.
Jaelani was killed together with his wife in an encounter on the slopes of a mountain in Bireuen district, they said.
The officials also claimed to have killed 18 other rebels in the latest round of fighting in the troubled province that lies in the northern tip of Sumatra islands.
The killings bring to nearly 900 the number of suspected GAM fighters who have died since May.
But a rebel spokesman has said he is unaware of the killings. The army has been accused of exaggerating its battlefield successes and committing extensive rights abuses in Aceh, where more than 35,000 troops are fighting about 5,000 rebels.
Rights activists allege that many of the suspected rebels killed are civilians who got caught in the crossfire.
The separatist rebels have been fighting for Aceh's independence from Indonesian rule since 1976. The resultant conflict has killed more than 10,000 people till this date.
The rebels have also been accused of rights violations by human rights groups.
Jakarta launched its military campaign against the GAM rebels after peace talks between the two collapsed.