Soldiers shot down five Free Aceh Movement separatists in clashes in northern Aceh on Wednesday, said Aceh military spokesman Ari Mulya Asnawi.
The other six were shot in three districts on Tuesday and Monday, Asnawi said.
The government on Friday is expected to announce a six-month extension of a civil emergency in Aceh - in which civilian authorities can order press censorship, curfews and other restrictions.
According to the Jakarta Post, the move to prolong the civil emergency state first imposed in May 2004 after a year of martial law, has already won full backing from parliament.
"We have no objection to the plan ... . The extension is necessary as we have to maintain the security situation in the province," the paper quoted the house speaker Agung Laksono as saying.
A military campaign against Free Aceh Movement (GAM) separatists, who have been fighting since 1976 for independence in Aceh, has continued despite the end of martial law.
Chief Security Minister Widodo Adi Sucipto said earlier this month that GAM remained a potent force which required the government to maintain troops in the resource-rich but impoverished province on the tip of Sumatra island.
He said about 2500 separatists with 850 weapons remained in Aceh. The military says thousands have been killed or captured or have surrendered, while rights groups say many of the casualties have been civilians.