Eight rebels were killed on Sunday and Saturday in operations which also saw four separatists arrested and 20 others surrendering, said military spokesman Ari Mulya Asnawi.
Ongoing violence on Monday saw an Indonesian private killed along with two separatists in a shootout, according to a second military spokesman, Edi Sulistiadie.
Troops shot down another rebel in a separate clash, he said.
The events mark the 28th anniversary of the separatist struggle.
A spokesmen for the Free Aceh Movement, founded on 4 December 1976, could not be reached for comment.
Ahead of the anniversary, the military said it would take tough action to prevent any celebrations on the anniversary, which in previous years has seen parades, flag-raisings and calls for a general strike.
An estimated 12,000 people - many of them civilians - have been killed since the rebels began their fight for the province on the tip of Sumatra island.
Rights groups accuse both sides of widespread abuses.
An estimated 12,000 people,
mostly civilians, have been killed
Peace talks between the government and separatists broke down in May 2003, and Jakarta launched a major military operation to crush the rebels.
The military says more than 2300 rebels have been killed since then.
Rights groups say many of the victims were civilians, a charge denied by the government.