An Indonesian military spokesman said two separatist rebels belonging to the Free Aceh Movement (GAM) were killed during a skirmish in the Aceh Tamiang district.
Government forces also claimed to have shot dead another rebel in Bireuen district, besides arresting six others in separate raids.
The latest killings come amid Jakarta's ongoing military offensive against the GAM rebels, who are seeking Aceh's independence from Indonesian rule.
Majority-Muslim Aceh, which lies on the northern tip of Sumatra islands, has been been swept by violence ever since the struggle for independence first erupted in 1976.
More than 10,000 people have died in the resultant conflict since then.
An Indonesian army official said on Saturday that 863 GAM rebels have been killed so far in the offensive that began on 19 May after peace talks between the two sides collapsed.
Another 1,800 rebels have either been arrested or surrendered in the intervening months. The army has lost 47 soldiers and the Indonesian police 15 officers.
Civilians have also been caught in the crossfire and the police say at least 319 civilians have been killed while 108 have gone missing.
The police did not say whether the army or the rebels are to blame for the civilian casualties.
Human rights groups have accused both sides of gross rights violations.